Oligonucleotide compositions with enhanced efficiency

ABSTRACT

The oligonucleotide compositions of the present invention make use of combinations of oligonucleotides. In one aspect, the invention features an oligonucleotide composition including at least 2 different oligonucleotides targeted to a target gene. This invention also provides methods of inhibiting protein synthesis in a cell and methods of identifying oligonucleotide compositions that inhibit synthesis of a protein in a cell.

RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No. 13/800,845filed Mar. 13, 2013, which is a continuation of U.S. application Ser.No. 12/630,523 filed Dec. 3, 2009, now abandoned, which application is acontinuation of U.S. application Ser. No. 10/357,826 filed Feb. 3, 2003,now abandoned, which application claims the benefit of U.S. ProvisionalApplication No. 60/353,381 filed Feb. 1, 2002. U.S. application Ser. No.10/357,826 also claims the benefit of U.S. Provisional Application No.60/353,203 filed on Feb. 1, 2002, U.S. Provisional Application No.60/436,238 filed Dec. 23, 2002, and U.S. Provisional Application No.60/438,608 filed Jan. 7, 2003. The entire contents of the aforementionedapplications are hereby expressly incorporated herein by reference intheir entirety as though fully set forth herein.

REFERENCE TO BIOLOGICAL SEQUENCE DISCLOSURE

This application contains nucleotide sequence and/or amino acid sequencedisclosure in computer readable form and a written sequence listing, theentire contents of both of which are expressly incorporated by referencein their entirety as though fully set forth herein.

BACKGROUND OF THE INVENTION

Antisense and double-stranded RNA oligonucleotides are promisingtherapeutic agents and useful research tools for elucidating genefunction. However, it is often difficult to achieve efficient inhibitionof protein synthesis using such compositions.

In order to maximize their therapeutic activity, it would be of greatbenefit to improve upon the prior art antisense and double-stranded RNAoligonucleotides by enhancing the efficiency with which they inhibitprotein synthesis.

SUMMARY OF THE INVENTION

The instant invention is based, at least in part, on the discovery ofantisense and double-stranded oligonucleotide compositions that provideimproved inhibition of gene expression. In particular, theoligonucleotide compositions of the present invention make use ofcombinations of antisense or double-stranded oligonucleotides.

In one aspect, the invention pertains to an oligonucleotide compositioncomprising at least 3 different oligonucleotides targeted to at leastthree different nucleotide sequences within a target gene, wherein (i)the oligonucleotides bind to their target nucleotide sequence with highaffinity and (ii) the oligonucleotides are GC enriched.

In one embodiment, the method is performed in a high-throughput format.

In another aspect, the invention pertains to a method of making theoligonucleotide composition, comprising: combining at least 3 differentoligonucleotides targeted to at least three different nucleotidesequences within a target gene, wherein (i) the oligonucleotides bind totheir target nucleotide sequence with high affinity and (ii) theoligonucleotides are GC enriched, and wherein the individualoligonucleotides are not separately tested for their ability to inhibitprotein synthesis prior to their incorporation into the composition.

In one embodiment, the oligonucleotides are antisense oligonucleotides.In another embodiment, the oligonucleotides are double-stranded RNAoligonucleotides.

In another aspect, the invention pertains to an oligonucleotidecomposition comprising at least 3 different double-stranded RNAoligonucleotides targeted to at least three different nucleotidesequences within a target gene.

In still another aspect, the invention pertains to a method ofinhibiting protein synthesis in a cell comprising contacting the cell(or cell lysate) with at least 3 different double-stranded RNAoligonucleotides targeted to at least three different nucleotidesequences within a target gene.

In yet another aspect, the invention pertains to a method of identifyingfunction of a gene encoding a protein comprising: contacting the cellwith at least 3 different double-stranded RNA oligonucleotides targetedto at least three different nucleotide sequences within a target geneand assaying for a change in a detectable phenotype in the cellresulting from the inhibition of protein expression, to therebydetermine the function of a gene.

In another aspect, the invention pertains to a method of making anoligonucleotide composition comprising combining at least 3 differentdouble-stranded RNA oligonucleotides targeted to at least threedifferent nucleotide sequences within a target gene wherein, theindividual oligonucleotides are not separately tested for their abilityto inhibit protein synthesis prior to their incorporation into thecomposition.

DRAWINGS

FIG. 1 shows a summary of the results of about 30 antisense inhibitionexperiments against about thirty different genes in cell culture.Oligonucleotide compositions comprising mixtures of oligonucleotides(with the worst 10% of target genes removed) are compared with the bestindividual oligonucleotides and data for all individual oligonucleotidesin the percent inhibition observed.

FIG. 2 shows ultramer data for a mixture of siRNA complexes targetingp53.

FIG. 3 shows ultramer data for a mixture of siRNA complexes targetingGTP20.

FIG. 4 shows ultramer data for a mixture of siRNA complexes targetingCbfa-1.

FIG. 5 shows data for a mixture of antisense oligonucleotides targetingPTP mu.

FIG. 6 shows data for a mixture of antisense oligonucleotides targetingPTP-PEST.

FIG. 7 shows data for a mixture of antisense oligonucleotides targetingPTP eta.

DETAILED DESCRIPTION OF THE INVENTION

Although inhibition of protein synthesis could be achieved with certainantisense and double-stranded RNA oligonucleotides of the prior art,multiple transfections were required to identify effectiveoligonucleotides. The instant invention advances the prior art, interalia, by providing oligonucleotide compositions that enhance theefficiency with which protein synthesis is inhibited and methods ofmaking and using these improved oligonucleotide compositions.

Methods of stabilizing oligonucleotides, particularly antisenseoligonucleotides, by formation of a duplex with a complementaryoligonucleotide, are disclosed in then co-pending U.S. application Ser.No. 10/357,529 filed on the same day as the priority application U.S.application Ser. No. 10/357,826, bearing attorney docket number“SRI-020,” and entitled “Double-Stranded Oligonucleotides.” Thisapplication and all of its teachings is hereby expressly incorporatedherein by reference in its entirety.

Antisense and Double-Stranded RNA Oligonucleotide Compositions

Antisense or double-stranded RNA oligonucleotides for incorporation intocompositions of the invention inhibit the synthesis of a target protein,which is encoded by a target gene. The target gene can be endogenous orexogenous (e.g., introduced into a cell by a virus or using recombinantDNA technology) to a cell. As used herein, the term “target gene”includes polynucleotides comprising a region that encodes a polypeptideor polynucleotide region that regulates replication, transcription,translation, or other process important in expression of the targetprotein or a polynucleotide comprising a region that encodes the targetpolypeptide and a region that regulates expression of the targetpolypeptide. Accordingly, the term “target gene” as used herein mayrefer to, for example, an mRNA molecule produced by transcription a geneof interest. Furthermore, the term “correspond,” as in “an oligomercorresponds to a target gene sequence,” means that the two sequences arecomplementary or homologous or bear such other biologically rationalrelationship to each other (e.g., based on the sequence ofnucleomonomers and their base-pairing properties).

The “target gene” to which an RNA molecule of the invention is directedmay be associated with a pathological condition. For example, the genemay be a pathogen-associated gene, e.g., a viral gene, atumor-associated gene, or an autoimmune disease-associated gene. Thetarget gene may also be a heterologous gene expressed in a recombinantcell or a genetically altered organism. By determining or modulating (eg., inhibiting) the function of such a gene, valuable information andtherapeutic benefits in medicine, veterinary medicine, and biology maybe obtained.

The term “antisense” refers to a nucleotide sequence that is invertedrelative to its normal orientation for transcription and so expresses anRNA transcript that is complementary to a target gene mRNA moleculeexpressed within the host cell (e.g., it can hybridize to the targetgene mRNA molecule through Watson-Crick base pairing). An antisensestrand may be constructed in a number of different ways, provided thatit is capable of interfering with the expression of a target gene. Forexample, the antisense strand can be constructed by inverting the codingregion (or a portion thereof) of the target gene relative to its normalorientation for transcription to allow the transcription of itscomplement, (e.g., RNAs encoded by the antisense and sense gene may becomplementary). Furthermore, the antisense oligonucleotide strand neednot have the same intron or exon pattern as the target gene, andnoncoding segments of the target gene may be equally effective inachieving antisense suppression of target gene expression as codingsegments.

The term “oligonucleotide” includes two or more nucleomonomerscovalently coupled to each other by linkages or substitute linkages. Anoligonucleotide may comprise, for example, between a few (e.g., 7, 10,12, 15) or a few hundred (e.g., 100, 200, 300, or 400) nucleomonomers.For example, an oligonucleotide of the invention preferably comprisesbetween about 10 and about 50 nucleomonomers, between about 15 and about40, or between about 20 and about 30 nucleomonomers. In one embodiment,an oligonucleotide comprises about 25 nucleomonomers. In anotherembodiment, an oligonucleotide comprises greater than about 25nucleomonomers.

Oligonucleotides may comprise, for example, oligonucleotides,oligonucleosides, polydeoxyribonucleotides (containing2′-deoxy-D-ribose) or modified forms thereof, e.g., DNA,polyribonucleotides (containing D-ribose or modified forms or analogsthereof), RNA, or any other type of polynucleotide which is anN-glycoside or C-glycoside of a purine or pyrimidine base, or modifiedpurine or pyrimidine base. The term oligonucleotide includescompositions in which adjacent nucleomonomers are linked viaphosphorothioate, amide or other linkages (e.g., Neilsen, P. E., et al.1991. Science. 254:1497). Generally, the term “linkage” refers to anyphysical connection, preferably covalent coupling, between two or morenucleic acid components, e.g., catalyzed by an enzyme such as a ligase.

The term “oligonucleotide” includes any structure that serves as ascaffold or support for the bases of the oligonucleotide, where thescaffold permits binding to the target nucleic acid molecule in asequence-dependent manner.

An “overhang” is a relatively short single-stranded nucleotide sequenceon the 5′- or 3′-hydroxyl end of a double-stranded oligonucleotidemolecule (also referred to as an “extension,” “protruding end,” or“sticky end”).

Oligonucleotides of the invention are isolated. The term “isolated”includes nucleic acid molecules which are synthesized (e.g., chemically,enzymatically, or recombinantly) or are naturally occurring butseparated from other nucleic acid molecules which are present in anatural source of the nucleic acid. Preferably, a naturally occurring“isolated” nucleic acid molecule is free of sequences which naturallyflank the nucleic acid molecule (i.e., sequences located at the 5′ and3′ ends of the nucleic acid molecule) in a nucleic acid molecule in anorganism from which the nucleic acid molecule is derived.

The term “nucleomonomer” includes bases covalently linked to a secondmoiety. Nucleomonomers include, for example, nucleosides andnucleotides. Nucleomonomers can be linked to form oligonucleotides thatbind to target nucleic acid sequences in a sequence specific manner. Theterm “second moiety” as used herein includes substituted andunsubstituted cycloalkyl moieties, e.g., cyclohexyl or cyclopentylmoieties, and substituted and unsubstituted heterocyclic moieties, e.g.,6-member morpholino moieties or, preferably, sugar moieties.

Sugar moieties include natural, unmodified sugars, e.g., monosaccharides(such as pentoses, e.g., ribose), modified sugars and sugar analogs.Possible modifications of nucleomonomers include, for example,replacement of one or more of the hydroxyl groups with a halogen, aheteroatom, an aliphatic group, or the functionalization of the group asan ether, an amine, a thiol, or the like. For example, modified sugarsinclude D-ribose, 2′-O-alkyl (including 2′-O-methyl and 2′-O-ethyl),i.e., 2′-alkoxy, 2′-amino, 2′-S-alkyl, 2′-halo (including 2′-fluoro),2′-methoxyethoxy, 2′-allyloxy (—OCH₂CH═CH₂), 2′-propargyl, 2′-propyl,ethynyl, ethenyl, propenyl, and cyano and the like. In one embodiment,the sugar moiety can be a hexose and incorporated into anoligonucleotide as described (Augustyns, K., et al., Nucl. Acids. Res.1992. 18:4711). Exemplary nucleomonomers can be found, e.g., in U.S.Pat. No. 5,849,902.

As used herein, the term “nucleotide” includes any monomeric unit of DNAor RNA containing a sugar moiety (pentose), a phosphate, and anitrogenous heterocyclic base. The base is usually linked to the sugarmoiety via the glycosidic carbon (at the 1′ carbon of pentose) and thatcombination of base and sugar is called a “nucleoside.” The basecharacterizes the nucleotide with the four customary bases of DNA beingadenine (A), guanine (G), cytosine (C) and thymine (T). Inosine (I) isan example of a synthetic base that can be used to substitute for any ofthe four, naturally-occurring bases (A, C, G or T). The four RNA basesare A, G, C, and uracil (U). Accordingly, an oligonucleotide may be anucleotide sequence comprising a linear array of nucleotides connectedby phosphodiester bonds between the 3′ and 5′ carbons of adjacentpentoses. Other modified nucleosides/nucleotides are described hereinand may also be used in the oligonucleotides of the invention.

One particularly useful group of modified nucleomonomers are 2′-O-methylnucleotides, especially when the 2′-O-methyl nucleotides are used asnucleomonomers in the ends of the oligomers. Such 2′O-methyl nucleotidesmay be referred to as “methylated,” and the corresponding nucleotidesmay be made from unmethylated nucleotides followed by alkylation ordirectly from methylated nucleotide reagents. Modified nucleomonomersmay be used in combination with unmodified nucleomonomers. For example,an oligonucleotide of the invention may contain both methylated andunmethylated nucleomonomers.

Some exemplary modified nucleomonomers include sugar-orbackbone-modified ribonucleotides. Modified ribonucleotides may containa nonnaturally occurring base (instead of a naturally occurring base)such as uridines or cytidines modified at the 5-position, e.g.,5-(2-amino)propyl uridine and 5-bromo uridine; adenosines and guanosinesmodified at the 8-position, e.g., 8-bromo guanosine; deaza nucleotides,e.g., 7-deaza-adenosine; and N-alkylated nucleotides, e.g., N6-methyladenosine. Also, sugar-modified ribonucleotides may have the 2′-OH groupreplaced by a H, alxoxy (or OR), R or alkyl, halogen, SH, SR, amino(such as NH₂, NHR, NR₂), or CN group, wherein R is lower alkyl, alkenyl,or alkynyl.

Modified ribonucleotides may also have the phosphoester group connectingto adjacent ribonucleotides replaced by a modified group, e.g., ofphosphothioate group. More generally, the various nucleotidemodifications may be combined.

The term “alkyl” includes saturated aliphatic groups, includingstraight-chain alkyl groups (e.g., methyl, ethyl, propyl, butyl, pentyl,hexyl, heptyl, octyl, nonyl, decyl, etc.), branched-chain alkyl groups(isopropyl, tert-butyl, isobutyl, etc.), cycloalkyl(alicyclic) groups(cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl), alkylsubstituted cycloalkyl groups, and cycloalkyl substituted alkyl groups.In certain embodiments, a straight chain or branched chain alkyl has 6or fewer carbon atoms in its backbone (e.g., C₁-C₆ for straight chain,C₃-C₆ for branched chain), and more preferably 4 or fewer. Likewise,preferred cycloalkyls have from 3-8 carbon atoms in their ringstructure, and more preferably have 5 or 6 carbons in the ringstructure. The term C₁-C₆ includes alkyl groups containing 1 to 6 carbonatoms.

Moreover, unless otherwise specified, the term alkyl includes both“unsubstituted alkyls” and “substituted alkyls,” the latter of whichrefers to alkyl moieties having substituents replacing a hydrogen on oneor more carbons of the hydrocarbon backbone. Such substituents caninclude, for example, alkenyl, alkynyl, halogen, hydroxyl,alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy,aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl,alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl,alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano,amino (including alkyl amino, dialkylamino, arylamino, diarylamino, andalkylarylamino), acylamino (including alkylcarbonylamino,arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl,alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl,sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido,heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.Cycloalkyls can be further substituted, e.g., with the substituentsdescribed above. An “alkylaryl” or an “arylalkyl” moiety is an alkylsubstituted with an aryl (e.g., phenylmethyl(benzyl)). The term “alkyl”also includes the side chains of natural and unnatural amino acids. Theterm “n-alkyl” means a straight chain (i.e., unbranched) unsubstitutedalkyl group.

The term “alkenyl” includes unsaturated aliphatic groups analogous inlength and possible substitution to the alkyls described above, but thatcontain at least one double bond. For example, the term “alkenyl”includes straight-chain alkenyl groups (e.g., ethylenyl, propenyl,butenyl, pentenyl, hexenyl, heptenyl, octenyl, nonenyl, decenyl, etc.),branched-chain alkenyl groups, cycloalkenyl(alicyclic) groups(cyclopropenyl, cyclopentenyl, cyclohexenyl, cycloheptenyl,cyclooctenyl), alkyl or alkenyl substituted cycloalkenyl groups, andcycloalkyl or cycloalkenyl substituted alkenyl groups. In certainembodiments, a straight chain or branched chain alkenyl group has 6 orfewer carbon atoms in its backbone (e.g., C₂-C₆ for straight chain,C₃-C₆ for branched chain). Likewise, cycloalkenyl groups may have from3-8 carbon atoms in their ring structure, and more preferably have 5 or6 carbons in the ring structure. The term C₂-C₆ includes alkenyl groupscontaining 2 to 6 carbon atoms.

Moreover, unless otherwise specified, the term alkenyl includes both“unsubstituted alkenyls” and “substituted alkenyls,” the latter of whichrefers to alkenyl moieties having substituents replacing a hydrogen onone or more carbons of the hydrocarbon backbone. Such substituents caninclude, for example, alkyl groups, alkynyl groups, halogens, hydroxyl,alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy,aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl,alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl,alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano,amino (including alkyl amino, dialkylamino, arylamino, diarylamino, andalkylarylamino), acylamino (including alkylcarbonylamino,arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl,alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl,sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido,heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

The term “alkynyl” includes unsaturated aliphatic groups analogous inlength and possible substitution to the alkyls described above, butwhich contain at least one triple bond. For example, the term “alkynyl”includes straight-chain alkynyl groups (e.g., ethynyl, propynyl,butynyl, pentynyl, hexynyl, heptynyl, octynyl, nonynyl, decynyl, etc.),branched-chain alkynyl groups, and cycloalkyl or cycloalkenylsubstituted alkynyl groups. In certain embodiments, a straight chain orbranched chain alkynyl group has 6 or fewer carbon atoms in its backbone(e.g., C₂-C₆ for straight chain, C₃-C₆ for branched chain). The termC₂-C₆ includes alkynyl groups containing 2 to 6 carbon atoms.

Moreover, unless otherwise specified, the term alkynyl includes both“unsubstituted alkynyls” and “substituted alkynyls,” the latter of whichrefers to alkynyl moieties having substituents replacing a hydrogen onone or more carbons of the hydrocarbon backbone. Such substituents caninclude, for example, alkyl groups, alkynyl groups, halogens, hydroxyl,alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy,aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl,alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl,alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano,amino (including alkyl amino, dialkylamino, arylamino, diarylamino, andalkylarylamino), acylamino (including alkylcarbonylamino,arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl,alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl,sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido,heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

Unless the number of carbons is otherwise specified, “lower alkyl” asused herein means an alkyl group, as defined above, but having from oneto five carbon atoms in its backbone structure. “Lower alkenyl” and“lower alkynyl” have chain lengths of, for example, 2-5 carbon atoms.

The term “alkoxy” includes substituted and unsubstituted alkyl, alkenyl,and alkynyl groups covalently linked to an oxygen atom. Examples ofalkoxy groups include methoxy, ethoxy, isopropyloxy, propoxy, butoxy,and pentoxy groups. Examples of substituted alkoxy groups includehalogenated alkoxy groups. The alkoxy groups can be substituted withgroups such as alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy,arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate,alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl,alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl,phosphate, phosphonato, phosphinato, cyano, amino (including alkylamino, dialkylamino, arylamino, diarylamino, and alkylarylamino),acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyland ureido), amidino, imino, sulfhydryl, alkylthio, arylthio,thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl,sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl,alkylaryl, or an aromatic or heteroaromatic moieties. Examples ofhalogen substituted alkoxy groups include, but are not limited to,fluoromethoxy, difluoromethoxy, trifluoromethoxy, chloromethoxy,dichloromethoxy, trichloromethoxy, etc.

The term “heteroatom” includes atoms of any element other than carbon orhydrogen. Preferred heteroatoms are nitrogen, oxygen, sulfur andphosphorus.

The term “hydroxy” or “hydroxyl” includes groups with an —OH or —O⁻(with an appropriate counterion).

The term “halogen” includes fluorine, bromine, chlorine, iodine, etc.The term “perhalogenated” generally refers to a moiety wherein allhydrogens are replaced by halogen atoms.

The term “substituted” includes substituents which can be placed on themoiety and which allow the molecule to perform its intended function.Examples of substituents include alkyl, alkenyl, alkynyl, aryl,(CR′R′)₀₋₃NR′R′, (CR′R′)₀₋₃CN, NO₂, halogen, (CR′R′)₀₋₃C(halogen)₃,(CR′R′)₀₋₃CH(halogen)₂, (CR′R′)₀₋₃CH₂(halogen), (CR′R′)₀₋₃CONR′R′,(CR′R′)₀₋₃S(O)₁₋₂NR′R′, (CR′R′)₀₋₃CHO, (CR′R′)₀₋₃O(CR′R′)₀₋₃H,(CR′R′)₀₋₃S(O)₀₋₂R′, (CR′R′)₀₋₃O(CR′R′)₀₋₃H, (CR′R′)₀₋₃COR′,(CR′R′)₀₋₃CO₂R′, or (CR′R′)₀₋₃OR′ groups; wherein each R′ and R′ areeach independently hydrogen, a C₁-C₅ alkyl, C₂-C₅ alkenyl, C₂-C₅alkynyl, or aryl group, or R′ and R′ taken together are a benzylidenegroup or a —(CH₂)₂O(CH₂)₂— group.

The term “amine” or “amino” includes compounds or moieties in which anitrogen atom is covalently bonded to at least one carbon or heteroatom.The term “alkyl amino” includes groups and compounds wherein thenitrogen is bound to at least one additional alkyl group. The term“dialkyl amino” includes groups wherein the nitrogen atom is bound to atleast two additional alkyl groups.

The term “ether” includes compounds or moieties which contain an oxygenbonded to two different carbon atoms or heteroatoms. For example, theterm includes “alkoxyalkyl” which refers to an alkyl, alkenyl, oralkynyl group covalently bonded to an oxygen atom which is covalentlybonded to another alkyl group.

The term “ester” includes compounds and moieties which contain a carbonor a heteroatom bound to an oxygen atom which is bonded to the carbon ofa carbonyl group. The term “ester” includes alkoxycarboxy groups such asmethoxycarbonyl, ethoxycarbonyl, propoxycarbonyl, butoxycarbonyl,pentoxycarbonyl, etc.

The term “base” includes the known purine and pyrimidine heterocyclicbases, deazapurines, and analogs (including heterocycl substitutedanalogs, e.g., aminoethyoxy phenoxazine), derivatives (e.g., 1-alkenyl-,1-alkynyl-, heteroaromatic-, and 1-alkynyl derivatives) and tautomersthereof. Examples of purines include adenine, guanine, inosine,diaminopurine, and xanthine and analogs (e.g., 8-oxo-N⁶-methyladenine or7-diazaxanthine) and derivatives thereof. Pyrimidines include, forexample, thymine, uracil, and cytosine, and their analogs (e.g.,5-methylcytosine, 5-methyluracil, 5-(1-propynyl)uracil,5-(1-propynyl)cytosine and 4,4-ethanocytosine). Other examples ofsuitable bases include non-purinyl and non-pyrimidinyl bases such as2-aminopyridine and triazines.

The term “nucleoside” includes bases which are covalently attached to asugar moiety, preferably ribose or deoxyribose. Examples of preferrednucleosides include ribonucleosides and deoxyribonucleosides.Nucleosides also include bases linked to amino acids or amino acidanalogs which may comprise free carboxyl groups, free amino groups, orprotecting groups. Suitable protecting groups are well known in the art(see P. G. M. Wuts and T. W. Greene, “Protective Groups in OrganicSynthesis”, 2^(nd) Ed., Wiley-Interscience, New York, 1999).

The term “nucleotide” includes nucleosides which further comprise aphosphate group or a phosphate analog.

In a preferred, embodiment, the nucleomonomers of an oligonucleotide ofthe invention are RNA nucleotides. In another preferred embodiment, thenucleomonomers of an oligonucleotide of the invention are modified RNAnucleotides.

As used herein, the term “linkage” includes a naturally occurring,unmodified phosphodiester moiety (—O—(PO₂ ⁻)—O—) that covalently couplesadjacent nucleomonomers. As used herein, the term “substitute linkage”includes any analog or derivative of the native phosphodiester groupthat covalently couples adjacent nucleomonomers. Substitute linkagesinclude phosphodiester analogs, e.g., such as phosphorothioate,phosphorodithioate, and P-ethyoxyphosphodiester, P-ethoxyphosphodiester,P-alkyloxyphosphotriester, methylphosphonate, and nonphosphoruscontaining linkages, e.g., such as acetals and amides. Such substitutelinkages are known in the art (e.g., Bjergarde et al. 1991. NucleicAcids Res. 19:5843; Caruthers et al. 1991. Nucleosides Nucleotides.10:47).

Oligonucleotides of the invention comprise 3′ and 5′ termini (except forcircular oligonucleotides). The 3′ and 5′ termini of an oligonucleotidecan be substantially protected from nucleases e.g., by modifying the 3′or 5′ linkages (e.g., U.S. Pat. No. 5,849,902 and WO 98/13526). Forexample, oligonucleotides can be made resistant by the inclusion of a“blocking group.” The term “blocking group” as used herein refers tosubstituents (e.g., other than OH groups) that can be attached tooligonucleotides or nucleomonomers, either as protecting groups orcoupling groups for synthesis (e.g., hydrogen phosphonate,phosphoramidite, or PO₃ ²⁻). “Blocking groups” also include “endblocking groups” or “exonuclease blocking groups” which protect the 5′and 3′ termini of the oligonucleotide, including modified nucleotidesand non-nucleotide exonuclease resistant structures.

Exemplary end-blocking groups include cap structures (e.g., a7-methylguanosine cap), inverted nucleomonomers, e.g., with 3′-3′ or5′-5′ end inversions (see e.g., Ortiagao et al. 1992. Antisense Res.Dev. 2:129), methylphosphonate, phosphoramidite, non-nucleotide groups(e.g., non-nucleotide linkers, amino linkers, conjugates) and the like.The 3′ terminal nucleomonomer can comprise a modified sugar moiety. The3′ terminal nucleomonomer can comprise a 3′-O that can optionally besubstituted by a blocking group that prevents 3′-exonuclease degradationof the oligonucleotide. For example, the 3′-hydroxyl can be esterifiedto a nucleotide through a 3′→3′ internucleotide linkage. For example,the alkyloxy radical can be methoxy, ethoxy, or isopropoxy, andpreferably, ethoxy. Optionally, the 3′→3′ linked nucleotide at the 3′terminus can be linked by a substitute linkage. To reduce nucleasedegradation, the 5′ most 3′→5′ linkage can be a modified linkage, e.g.,a phosphorothioate or a P-alkyloxyphosphotriester linkage. Preferably,the two 5′ most 3′→5′ linkages are modified linkages. Optionally, the 5′terminal hydroxy moiety can be esterified with a phosphorus containingmoiety, e.g., phosphate, phosphorothioate, or P-ethoxyphosphate.

In one embodiment, an oligonucleotide may comprise a 5′ phosphate groupor a group larger than a phosphate group.

In one embodiment, the oligonucleotides included in the composition arehigh affinity oligonucleotides. The term “high affinity” as used hereinincludes oligonucleotides that have a Tm (melting temperature) of orgreater than about 60° C., greater than about 65° C., greater than about70° C., greater than about 75° C., greater than about 80° C. or greaterthan about 85° C. The Tm is the midpoint of the temperature range overwhich the oligonucleotide separates from the target nucleotide sequence.At this temperature, 50% helical (hybridized) versus coil (unhybridized)forms are present. Tm is measured by using the UV spectrum to determinethe formation and breakdown (melting) of hybridization. Base stackingoccurs during hybridization, which leads to a reduction in UVabsorption. Tm depends both on GC content of the two nucleic acidmolecules and on the degree of sequence complementarity. Tm can bedetermined using techniques that are known in the art (see for example,Monia et al. 1993. J. Biol. Chem. 268:145; Chiang et al. 1991. J. Biol.Chem. 266:18162; Gagnor et al. 1987. Nucleic Acids Res. 15:10419; Moniaet al. 1996. Proc. Natl. Acad. Sci. 93:15481; Publisis and Tinoco. 1989.Methods in Enzymology 180:304; Thuong et al. 1987. Proc. Natl. Acad.Sci. USA 84:5129).

One skilled in the art will recognize that the length of an RNAioligonucleotide corresponds to a region of complementarity to the targetin the antisense stranded, and the RNAi may be longer, if, for examplethe RNAi is of a hairpin design.

In one embodiment, an oligonucleotide can include an agent whichincreases the affinity of the oligonucleotide for its target sequence.The term “affinity enhancing agent” includes agents that increase theaffinity of an oligonucleotide for its target. Such agents include,e.g., intercalating agents and high affinity nucleomonomers.Intercalating agents interact strongly and nonspecifically with nucleicacids. Intercalating agents serve to stabilize RNA-DNA duplexes and thusincrease the affinity of the oligonucleotides for their targets.Intercalating agents are most commonly linked to the 3′ or 5′ end ofoligonucleotides. Examples of intercalating agents include: acridine,chlorambucil, benzopyridoquinoxaline, benzopyridoindole,benzophenanthridine, and phenazinium. The agents may also impart othercharacteristics to the oligonucleotide, for example, increasingresistance to endonucleases and exonucleases.

In one embodiment, a high affinity nucleomonomer is incorporated into anoligonucleotide. The language “high affinity nucleomonomer” as usedherein includes modified bases or base analogs that bind to acomplementary base in a target nucleic acid molecule with higheraffinity than an unmodified base, for example, by having moreenergetically favorable interactions with the complementary base, e.g.,by forming more hydrogen bonds with the complementary base. For example,high affinity nucleomonomer analogs such as aminoethyoxy phenoxazine(also referred to as a G clamp), which forms four hydrogen bonds withguanine are included in the term “high affinity nucleomonomer.” A highaffinity nucleomonomer is illustrated below (see, e.g., Flanagan, etal., 1999. Proc. Natl. Acad. Sci. 96:3513).

Other exemplary high affinity nucleomonomers are known in the art andinclude 7-alkenyl, 7-alkynyl, 7-heteroaromatic-, or7-alkynyl-heteroaromatic-substituted bases or the like which can besubstituted for adenosine or guanosine in oligonucleotides (see e.g.,U.S. Pat. No. 5,594,121). Also, 7-substituted deazapurines have beenfound to impart enhanced binding properties to oligonucleotides, i.e.,by allowing them to bind with higher affinity to complementary targetnucleic acid molecules as compared to unmodified oligonucleotides. Highaffinity nucleomonomers can be incorporated into the oligonucleotides ofthe instant invention using standard techniques.

In another embodiment, an agent that increases the affinity of anoligonucleotide for its target comprises an intercalating agent. As usedherein the language “intercalating agent” includes agents which can bindto a DNA double helix. When covalently attached to an oligonucleotide ofthe invention, an intercalating agent enhances the binding of theoligonucleotide to its complementary genomic DNA target sequence. Theintercalating agent may also increase resistance to endonucleases andexonucleases. Exemplary intercalating agents are taught by Helene andThuong (1989. Genome 31:413), and include e.g., acridine derivatives(Lacoste et al. 1997. Nucleic Acids Research. 25:1991; Kukreti et al.1997. Nucleic Acids Research. 25:4264); quinoline derivatives (Wilson etal. 1993. Biochemistry 32:10614); benzo[f]quino[3,4-b]quioxalinederivatives (Marchand et al. 1996. Biochemistry. 35:5022; Escude et al.1998. Proc. Natl. Acad. Sci. 95:3591). Intercalating agents can beincorporated into an oligonucleotide using any convenient linkage. Forexample, acridine or psoralen can be linked to the oligonucleotidethrough any available —OH or —SH group, e.g., at the terminal 5′position of the oligonucleotide, the 2′ positions of sugar moieties, oran OH, NH₂, COOH or SH incorporated into the 5-position of pyrimidinesusing standard methods.

In one embodiment, when included in an RNase H activating antisenseoligonucleotide, an agent that increases the affinity of anoligonucleotide for its target is not positioned adjacent to an RNaseactivating region of the oligonucleotide, e.g., is positioned adjacentto a non-RNase activating region. Preferably, the agent that increasesthe affinity of an oligonucleotide for its target is placed at adistance as far as possible from the RNase activating domain of thechimeric antisense oligonucleotide such that the specificity of thechimeric antisense oligonucleotide is not altered when compared with thespecificity of a chimeric antisense oligonucleotide which lacks theintercalating compound. In one embodiment, this can be accomplished bypositioning the agent adjacent to a non-RNase activating region. Thespecificity of the oligonucleotide can be tested by demonstrating thattranscription of a non-target sequence. Preferably a non-target sequencewhich is structurally similar to the target (e.g., has some sequencehomology or identity with the target sequence but which is not identicalin sequence to the target) is not inhibited to a greater degree by anoligonucleotide comprising an affinity enhancing agent directed againstthe target than by an oligonucleotide that does not comprise an affinityenhancing agent that is directed against the target.

In one embodiment, the oligonucleotides of the invention are GCenriched. As used herein the term “GC enriched” includesoligonucleotides that have a relatively high percent GC content. Forexample, in one embodiment an oligonucleotide of the invention has atleast about 20%, at least about 30%, at least about 40% GC content. Inanother embodiment, an oligonucleotide of the invention has at leastabout 50%, at least about 60%, or at least about 70% GC content.

In one embodiment, the oligonucleotides of the invention are at leastabout 25 nucleomonomers in length. In one embodiment, the antisenseoligonucleotides of the invention are greater than about 25nucleomonomers in length. In one embodiment, an antisenseoligonucleotide of the invention is at least about 30, at least about40, at least about 50, or at least about 60, at least about 70, at leastabout 80, or at least about 90 nucleomonomers in length.

Double-Stranded RNA Oligonucleotides

Double-stranded RNA (double-stranded RNA or RNAi (double-stranded RNAinterference)) is a double-stranded RNA oligonucleotide that can be usedto inhibit protein synthesis in a cell (see, e.g., WO 01/36646A1;Elbashir et al. 2001. Genes & Development 15:188; Elbashir et al. 2001.Nature 411:494; Elbashir et al. 2001 EMBO. 20:6877). Double-stranded RNAmay be formed by a single, self-complementary strand or two separatecomplementary strands. Duplex formation can occur either inside oroutside the cell containing the target gene.

As used herein, the term “double-stranded” includes one or more nucleicacid molecules comprising a region of the molecule in which at least aportion of the nucleomonomers are complementary and hydrogen bond toform a duplex.

As used herein, the term “duplex” includes the region of thedouble-stranded nucleic acid molecule(s) that is (are) hydrogen bondedto a complementary sequence.

Accordingly, one aspect of the invention is a method of inhibiting theactivity of a target gene by introducing an RNAi agent into a cell, suchthat the dsRNA component of the RNAi agent is targeted to the gene. Inone embodiment, an RNA oligonucleotide molecule may contain at least onenucleomonomer that is a modified nucleotide analogue. The nucleotideanalogues may be located at positions where the target-specificactivity, e.g., the RNAi mediating activity is not substantiallyeffected, e.g., in a region at the 5′-end or the 3′-end of thedouble-stranded molecule, where the overhangs may be stabilized byincorporating modified nucleotide analogues.

In another aspect, double-stranded RNA molecules known in the art can beused in the methods of the present invention. Double-stranded RNAmolecules known in the art may also be modified according to theteachings herein in conjunction with such methods, e.g., by usingmodified nucleomonomers. For example, see U.S. Pat. No. 6,506,559; U.S.2002/0,173,478 A1; U.S. 2002/0,086,356 Al; Shuey, et al., “RNAi:gene-silencing in therapeutic intervention.” Drug Discov. Today 2002Oct. 15; 7(20):1040-6; Aoki, et al., “Clin. Exp. Pharmacol. Physiol.2003 January; 30(1-2):96-102; Cioca, et al., “RNA interference is afunctional pathway with therapeutic potential in human myeloid leukemiacell lines. Cancer Gene Ther. 2003 February; 10 (2):125-33.

Further examples of double-stranded RNA molecules include thosedisclosed in the following references: Kawasaki, et al., “Short hairpintype of dsRNAs that are controlled by tRNA(Val) promoter significantlyinduce RNAi-mediated gene silencing in the cytoplasm of human cells.”Nucleic Acids Res. 2003 Jan. 15; 31(2):700-7; Cottrell, et al., “Silenceof the strands: RNA interference in eukaryotic pathogens.” TrendsMicrobiol. 2003 January; 11(1):37-43; Links, “Mammalian RNAi for themasses.” Trends Genet. 2003 January; 19(1):9-12; Hamada, et al.,“Effects on RNA interference in gene expression (RNAi) in culturedmammalian cells of mismatches and the introduction of chemicalmodifications at the 3′-ends of siRNAs.” Antisense Nucleic Acid DrugDev. 2002 October; 12(5):301-9; Links, “RNAi and related mechanisms andtheir potential use for therapy.” Curr. Opin. Chem. Biol. 2002 December;6(6):829-34; Kawasaki, et al., “Short hairpin type of dsRNAs that arecontrolled by tRNA(Val) promoter significantly induce RNAi-mediated genesilencing in the cytoplasm of human cells.” Nucleic Acids Res. 2003 Jan.15; 31(2):700-7.)

Double-stranded RNA molecule comprises a nucleotide sequence which issubstantially identical to at least part of the target gene. In oneembodiment, a double-stranded RNA molecule comprises a nucleotidesequence which is at least about 100% identical to a portion of thetarget gene. In another embodiment, a double-stranded RNA moleculecomprises a nucleotide sequence which is at least about 95% identical toa portion of the target gene. In another embodiment, a double-strandedRNA molecule comprises a nucleotide sequence which is at least about 90%identical to a portion of the target gene. In another embodiment, adouble-stranded RNA molecule comprises a nucleotide sequence which is atleast about 80% identical to a portion of the target gene. In anotherembodiment, a double-stranded RNA molecule comprises a nucleotidesequence which is at least about 60% identical to a portion of thetarget gene. In another embodiment, a double-stranded RNA moleculecomprises a nucleotide sequence which is at least about 100% identicalto a portion of the target gene.

To determine the percent identity of two nucleic acid sequences, thesequences are aligned for optimal comparison purposes (e.g., gaps can beintroduced in one or both of a first and a second amino acid or nucleicacid sequence for optimal alignment and non-identical sequences can bedisregarded for comparison purposes). In a preferred embodiment, thelength of the target gene sequence aligned for comparison purposes is atleast about 25 nucleotide residues, at least about 50, at least about100, at least about 150, at least about 200, or at least about 300 ormore nucleotide residues are aligned. The nucleotides at correspondingnucleotide positions are then compared. When a position in the firstsequence is occupied by the same nucleotide as the correspondingposition in the second sequence, then the molecules are identical atthat position. The percent identity between the two sequences is afunction of the number of identical positions shared by the sequences,taking into account the number of gaps, and the length of each gap,which need to be introduced for optimal alignment of the two sequences.

The comparison of sequences and determination of percent identitybetween two sequences can be accomplished using a mathematicalalgorithm. In a preferred embodiment, the percent identity between twonucleotide sequences is determined using e.g., the GAP program in theGCG software package, using a NWSgapdna. CMP matrix and a gap weight of40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. Inanother embodiment, the percent identity between two nucleotidesequences is determined using the algorithm of E. Meyers and W. Miller(Comput. Appl. Biosci. 4:11-17 (1988)) which has been incorporated intothe ALIGN program (version 2.0), using a PAM120 weight residue table, agap length penalty of 12 and a gap penalty of 4.

The nucleic acid sequences of the present invention can further be usedas a “query sequence” to perform alignments against sequences in publicdatabases. Such searches can be performed using the NBLAST and XBLASTprograms (version 2.0) of Altschul et al. (1990) J. Mol. Biol.215:403-10. BLAST nucleotide searches can be performed with the NBLASTprogram, score=100, wordlength=12. To obtain gapped alignments forcomparison purposes, Gapped BLAST can be utilized as described inAltschul et al. (1997) Nucleic Acids Res. 25(17):3389-3402. Whenutilizing BLAST and Gapped BLAST programs, the default parameters of therespective programs (e.g., XBLAST and NBLAST) can be used. See, e.g.,the NIH internet website.

In one embodiment, the oligonucleotides of the invention are identicalto a target nucleic acid sequence over at least about 80% of the lengthof the oligonucleotide. In another embodiment, oligonucleotides of theinvention are identical to a target nucleic acid sequence over at leastabout 90-95% of the length of the oligonucleotide. In anotherembodiment, oligonucleotides of the invention are identical to a targetnucleic acid sequence over the entire length of the oligonucleotide.

In yet another embodiment, a sequence of a double-stranded RNA moleculeof the invention hybridizes to at least a portion of the target geneunder stringent hybridization conditions. As used herein, the term“hybridizes under stringent conditions” is intended to describeconditions for hybridization and washing under which nucleotidesequences at least 60% complementary to each other typically remainhybridized to each other. Preferably, the conditions are such thatsequences at least about 70%, more preferably at least about 80%, evenmore preferably at least about 85% or 90% complementary to each othertypically remain hybridized to each other. Such stringent conditions areknown to those skilled in the art and can be found in Current Protocolsin Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Apreferred, non-limiting example of stringent hybridization conditionsare hybridization in 6× sodium chloride/sodium citrate (SSC) at about45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 50° C.,preferably at 55° C., more preferably at 60° C., and even morepreferably at 65° C. Ranges intermediate to the above-recited values,e.g., at 60-65° C. or at 55-60° C. are also intended to be encompassedby the present invention. Alternatively, formamide can be included inthe hybridization solution, using methods and conditions also known inthe art.

Antisense Oligonucleotides

As used herein, the term “antisense oligonucleotide” includesoligonucleotides which comprise a nucleotide sequence which isspecifically interferes with the synthesis of the target polypeptide. Ingeneral, antisense oligonucleotides of the invention bind to the “sense”strand of the nucleotide sequence of the target gene (e.g.,polynucleotides such as DNA, mRNA (including pre-mRNA)) molecules. Whenantisense oligonucleotides of the invention bind to nucleic acidmolecules, they can bind to any region of the nucleic acid molecule,including e.g., introns, exons, 5′, or 3′ untranslated regions. Forexample, antisense oligonucleotides that work as steric blockerspreferentially bind within a splice junction, 5′ untranslated region, orthe start region of a nucleic acid target molecule. Antisenseoligonucleotides that work by activating RNase H preferably bind withinan intron, an exon, the 5′ untranslated region, or the 3′ untranslatedregion of a nucleic acid target molecule.

Antisense oligonucleotides of the invention may or may not becomplementary to their target sequence. Without being limited to anyparticular mechanism of action, an antisense oligonucleotide used in anoligonucleotide composition of the invention that can specificallyhybridize with a nucleotide sequence within the target gene (i.e., iscomplementary to a nucleotide sequence within the target gene) mayachieve its affects based on, e.g., (1) binding to target mRNA andstericly blocking the ribosome complex from translating the mRNA; (2)binding to target mRNA and triggering mRNA cleavage by RNase H; (3)binding to double-stranded DNA in the nucleus and forming a triplehelix; (4) hybridizing to open DNA loops created by RNA polymerase; (5)interfering with mRNA splicing; (6) interfering with transport of mRNAfrom the nucleus to the cytoplasm; or (7) interfering with translationthrough inhibition of the binding of initiation factors or assembly ofribosomal subunits (i.e., at the start codon).

Without being limited to any particular mechanism of action, theantisense oligonucleotides used in an oligonucleotide composition of theinvention that cannot specifically hybridize with a nucleotide sequencewithin the target gene (are not complementary to a nucleotide sequencewithin the target gene) may achieve their affects based on, e.g., (1)the secondary structure of the oligonucleotide; (2) hybridization to adifferent nucleotide sequence; (3) binding to proteins or othermolecules that may affect the target gene; or (4) modulatingoligonucleotide degradation products which themselves can affectcellular functions.

In one embodiment, at least two of the antisense oligonucleotides in anoligonucleotide composition of the invention inhibit protein synthesisvia the same mechanism. In another embodiment, at least two of theantisense oligonucleotides in an oligonucleotide composition inhibitprotein synthesis via a different mechanism. In yet another embodiment,all of the antisense oligonucleotides present in an oligonucleotidecomposition inhibit protein synthesis via the same mechanism. Theoligonucleotide compositions of the present invention may compriseantisense oligonucleotides which rely simultaneously on several of thesemodes of action.

The antisense oligonucleotides used in an oligonucleotide composition ofthe invention may be of any type, e.g., including morpholinooligonucleotides, RNase H activating oligonucleotides, or ribozymes.

In one embodiment, antisense oligonucleotides of the invention aresubstantially complementary to a target nucleic acid sequence. Percentcomplementarity is determined analogously to percent identity. Forexample, when a position in a test nucleotide sequence is occupied by anucleotide that is complementary to the corresponding position in thereference sequence, then the molecules are complementary at thatposition. In one embodiment, an antisense RNA molecule comprises anucleotide sequence which is at least about 100% complementary to aportion of the target gene. In another embodiment, an antisense RNAmolecule comprises a nucleotide sequence which is at least about 90%complementary to a portion of the target gene. In another embodiment, anantisense RNA molecule comprises a nucleotide sequence which is at leastabout 80% complementary to a portion of the target gene. In anotherembodiment, an antisense RNA molecule comprises a nucleotide sequencewhich is at least about 60% complementary to a portion of the targetgene. In another embodiment, an antisense RNA molecule comprises anucleotide sequence which is at least about 100% complementary to aportion of the target gene. Preferably, no loops greater than about 8nucleotides are formed by areas of non-complementarity between theoligonucleotide and the target.

In one embodiment, the antisense oligonucleotides of the invention arecomplementary to a target nucleic acid sequence over at least about 80%of the length of the oligonucleotide. In another embodiment, antisenseoligonucleotides of the invention are complementary to a target nucleicacid sequence over at least about 90-95% of the length of theoligonucleotide. In another embodiment, antisense oligonucleotides ofthe invention are complementary to a target nucleic acid sequence overthe entire length of the oligonucleotide.

Antisense oligonucleotides of the invention can be “chimericoligonucleotides” which comprise an RNA-like and a DNA-like region. Thelanguage “RNase H activating region” includes a region of anoligonucleotide, e.g., a chimeric oligonucleotide, that is capable ofrecruiting RNase H to cleave the target RNA strand to which theoligonucleotide binds. Typically, the RNase activating region contains aminimal core (of at least about 3-5, typically between about 3-12, moretypically, between about 5-12, and more preferably between about 5-10contiguous nucleomonomers) of DNA or DNA-like nucleomonomers. (See e.g.,U.S. Pat. No. 5,849,902). More preferably, the RNase H activating regioncomprises about nine contiguous deoxyribose containing nucleomonomers.Preferably, the contiguous nucleomonomers are linked by a substitutelinkage, e.g., a phosphorothioate linkage.

The language “non-activating region” includes a region of an antisenseoligonucleotide, e.g., a chimeric oligonucleotide, that does not recruitor activate RNase H. Preferably, a non-activating region does notcomprise phosphorothioate DNA. The oligonucleotides of the inventioncomprise at least one non-activating region. In one embodiment, thenon-activating region can be stabilized against nucleases or can providespecificity for the target by being complementary to the target andforming hydrogen bonds with the target nucleic acid molecule, which isto be bound by the oligonucleotide.

Antisense oligonucleotides of the present invention may include“morpholino oligonucleotides.” Morpholino oligonucleotides are non-ionicand function by an RNase H-independent mechanism. Each of the 4 geneticbases (Adenine, Cytosine, Guanine, and Thymine/Uracil) of the morpholinooligonucleotides is linked to a 6-membered morpholine ring. Morpholinooligonucleotides are made by joining the 4 different subunit types bynon-ionic phosphorodiamidate intersubunit linkages. An example of a 2subunit morphilio oligonucleotide is shown below.

Morpholino oligonucleotides have many advantages including completeresistance to nucleases (Antisense & Nuc. Acid Drug Dev. 1996. 6:267);predictable targeting (Biochemica Biophysica Acta. 1999. 1489:141);reliable activity in cells (Antisense & Nuc. Acid Drug Dev. 1997. 7:63);excellent sequence specificity (Antisense & Nuc. Acid Drug Dev. 1997.7:151); minimal non-antisense activity (Biochemica Biophysica Acta.1999. 1489:141); and simple osmotic or scrape delivery (Antisense & Nuc.Acid Drug Dev. 1997. 7:291). Morpholino oligonucleotides are alsopreferred because of their non-toxicity at high doses. A discussion ofthe preparation of morpholino oligonucleotides can be found in Antisense& Nuc. Acid Drug Dev. 1997. 7:187.

A variety of nucleotides of different lengths may be used. In oneembodiment, an oligonucleotide of the invention is greater than about 25nucleomonomers in length. In one embodiment, an oligonucleotide of theinvention is at least about 10, 12, 14, 16, 18, 20, 22, 24, 26, 27, 28,29, 30, at least about 40, at least about 50, or at least about 60, atleast about 70, at least about 80, or at least about 90 nucleomonomersin length. In another embodiment, an oligonucleotide of the invention isless than about 25 nucleomonomers in length, particularly about 21 to23. In yet another embodiment, an oligonucleotide of the invention isabout 10, 12, 14, 16, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30nucleomonomers in length. In another embodiment, an oligonucleotide ofthe invention is at most about 26, 27, 28, 29, 30, at most about 40, atmost about 50, or at most about 60, at most about 70, at most about 80,or at most about 90 nucleomonomers in length.

Preferred nucleomonomers in some aspects are ribonucleotides, including2′-O-methyl ribonucleotides and other 2′-modified RNA molecules.

Oligomers of the invention may also comprise a DNA gap or aphosphorothioate DNA gap.

In some aspects, the present invention relates to compositions andmethods comprising at least about 4, 5, 6, 7, 8, 9, or 10 antisenseoligonucleotides targeting at least four, five, six, seven, eight, nine,or ten different nucleic acid sequences.

Selection of Oligonucleotide Sequences

Once the target protein is selected and the nucleotide sequence whichencodes it is determined, the sequence of an oligonucleotide forinclusion in the compositions of the invention is determined. Thesequence of the target gene is analyzed and oligonucleotides are chosenby a process including both elimination and selection steps. In oneembodiment, oligonucleotides which have more than 3 of any nucleotide(A, U, C, or G) occurring consecutively within the oligonucleotide areeliminated. In another embodiment, oligonucleotides having dinucleotiderepeats (e.g., AUAU, ACAC, AGAG, UCUC, UGUG, or CGCG) are eliminated. Inanother embodiment, oligonucleotides are chosen that target nucleotidesequences of the target gene that are preferably at least about 25nucleotides apart. In another embodiment, oligonucleotides are chosenthat comprise between 4 and 10 (inclusive) of each base, such that thebase composition of the oligonucleotides is similar. In anotherembodiment, the percentage of bases in the oligonucleotide which are Gor C is greater than 50%. In one embodiment, when oligonucleotides aredesigned to be complementary to a chosen target sequence, preferably,they are 100% complementary to the target sequence. In anotherembodiment, an oligonucleotide preferably has greater than 2 mismatchesto other, non-target genes. This can be tested by one of ordinary skillin the art, e.g., using available alignment programs and publicdatabases, e.g., the National Institutes of Health internet website.

Oligonucleotide Compositions of the Invention

This invention relates to oligonucleotide compositions including morethan one individual oligonucleotide molecule. The individualoligonucleotide molecules of the composition target at least one targetnucleotide sequence of a single target gene. For example, in oneembodiment, at least two of the oligonucleotides present in thecomposition target the same nucleotide sequence in the same target genee.g., the oligonucleotides comprise different chemistries but target(e.g., specifically hybridize to) the same sequence of bases in a targetnucleic acid molecule. In another embodiment, at least two of theoligonucleotides present in the composition target different nucleotidesequences in the same target gene (e.g., the oligonucleotide compositioncomprises one oligonucleotide targeting a nucleotide sequence in thepromoter of a gene and another oligonucleotide targeting a nucleotidesequence in the portion of the coding sequence of the target nucleicacid molecule or the oligonucleotide composition comprises at least twodifferent oligonucleotides that target two different nucleotidesequences in the coding region of the target nucleic acid molecule).

The number of oligonucleotides used in an oligonucleotide composition ofthe invention can vary from as few as about 2 oligonucleotides togreater than about 20 oligonucleotides. In one embodiment, at leastabout 3-4 different oligonucleotides are used in the oligonucleotidecomposition. In another embodiment, at least about 5-6 differentoligonucleotides are used in the oligonucleotide composition. In afurther embodiment, at least about 7-8 different oligonucleotides areused in the oligonucleotide composition. In one embodiment, greater thanabout 8 different oligonucleotides are used in an oligonucleotidecomposition of the invention. In a preferred embodiment, the number ofdifferent oligonucleotides in the oligonucleotide composition is chosenso as to use the minimum number of different oligonucleotides thateffectively inhibit synthesis of the target protein.

The different oligonucleotides used in an oligonucleotide composition ofthe invention can each be present at the same concentration or can bepresent in different concentrations. For example, more desirableoligonucleotides (e.g., those that are more inexpensive or easier tosynthesize) may be present at higher concentrations than less desirableoligonucleotides.

Preferably, the oligonucleotides in a composition are either alldouble-stranded RNA oligonucleotides or all antisense oligonucleotides.

It will be understood that the individual oligonucleotides of theinvention can be synthesized to comprise different chemistries. Forexample, in one embodiment, a composition of the invention can compriseat least one oligonucleotide that is optionally GC enriched. In anotherembodiment, a composition of the invention comprises at least oneoligonucleotide that binds to its target with high affinity. In anotherexemplary embodiment, a composition of the invention comprises at leastone that is at least about 25 nucleomonomers in length. In oneembodiment, an oligonucleotide of the invention comprises anoligonucleotide that is GC enriched and binds to its target with highaffinity. Thus, as shown by this example, one of skill in the art willrecognize that given the teachings of the specification, multiplevariations of the individual oligonucleotides present in improvedoligonucleotide compositions of the invention can be made.

Making Oligonucleotide Compositions

In one embodiment, an individual oligonucleotide is not individuallytested for its ability to inhibit protein synthesis prior to itsinclusion into a composition of the invention.

In another embodiment, an individual oligonucleotide for inclusion in anoligonucleotide composition inhibits protein synthesis by about 20% whentested individually. In another embodiment, an individualoligonucleotide for inclusion in an oligonucleotide composition inhibitsgene expression by about 30% when tested individually. In anotherembodiment, an individual oligonucleotide for inclusion in anoligonucleotide composition inhibits gene expression by about 40% whentested individually. In another embodiment, an individualoligonucleotide for inclusion in an oligonucleotide composition inhibitsgene expression by about 50% when tested individually. In anotherembodiment, an individual oligonucleotide for inclusion in anoligonucleotide composition inhibits gene expression by about 60% whentested individually. Preferably, an individual oligonucleotide forinclusion in an oligonucleotide composition inhibits gene expression byless than about 40% when tested individually.

In one embodiment, an oligonucleotide composition of the inventioninhibits gene expression to an extent that is greater than the level ofinhibition of gene expression achieved by any of the individualoligonucleotides of the oligonucleotide composition acting alone. Inanother embodiment, the oligonucleotide composition achieves a level ofinhibition of protein synthesis the same as or higher than the level ofinhibition achieved by the most effective individual oligonucleotide ofthe composition. In one embodiment, an oligonucleotide composition ofthe present invention is at least about 80% effective at inhibiting geneexpression. In another embodiment, an oligonucleotide composition of thepresent invention is at least about 90%-95% effective at inhibiting geneexpression. In another embodiment, an oligonucleotide composition of thepresent invention is at least about 99% effective at inhibiting geneexpression.

The subject compositions greatly increase the efficiency of theinhibition of protein synthesis because the ability of an individualoligonucleotide to inhibit protein synthesis does not have to be testedprior to its inclusion in an oligonucleotide composition of theinvention. Accordingly, only one transfection need be done toeffectively inhibit protein synthesis. Thus, in one embodiment, anoligonucleotide composition of the invention is contacted with a cell orpopulation of cells prior to testing the ability of the individualoligonucleotides of the composition to inhibit target gene expression.In another embodiment, an oligonucleotide composition of the inventionis contacted with a cell or population of cells subsequent to testingthe ability of the individual oligonucleotides of the composition toinhibit target gene expression.

To achieve inhibition of gene expression, an oligonucleotide compositionof the invention is contacted with a cell (or cell lysate). In oneembodiment, the oligonucleotides of an oligonucleotide composition arecontacted with a cell simultaneously. In an alternative embodiment, theoligonucleotides of an oligonucleotide composition can be brought intocontact with a cell at different times. For example, at least one of theoligonucleotides can be contacted with a cell at a different time fromthe other oligonucleotides. In yet another example, each of theoligonucleotides of an oligonucleotide composition is contacted with acell sequentially so that each of the oligonucleotides of anoligonucleotide composition comes into contact with the cell at adifferent time. As such, the compositions of the instant invention canbe formulated for separate administration of the oligonucleotides.Preferably, a cell is contacted with oligonucleotides of the inventionsuch that the level of inhibition of protein synthesis (e.g., asmeasured either directly (by measuring the decrease in the amount of thetarget protein produced) or, for example, by measuring the disappearanceof a phenotype associated with the presence of the target protein, bymeasuring a reduction in the amount of mRNA produced from the targetgene, or by measuring in increase in the level of degradation of themRNA) is greater than that observed when individual nucleotides of theinvention are tested individually.

The number of oligonucleotides used to contact a cell can vary from asfew as 2 oligonucleotides to greater than about 20 oligonucleotides. Inone embodiment, at least about 2-3 different oligonucleotides arecontacted with a cell. In another embodiment, at least about 4-5different oligonucleotides are used to contact the cell. In a furtherembodiment, at least about 6-7 different oligonucleotides are contactedwith a cell.

The ability of an oligonucleotide composition of the invention toinhibit protein synthesis can be measured using techniques which areknown in the art, for example, by detecting an inhibition in genetranscription or protein synthesis. For example, Nuclease S1 mapping canbe performed. In another example, Northern blot analysis can be used tomeasure the presence of RNA encoding a particular protein. For example,total RNA can be prepared over a cesium chloride cushion (see, e.g.,Ausebel et al., eds. 1987 Current Protocols in Molecular Biology, Greene& Wiley, New York). Northern blots can then be made using the RNA andprobed (see, e.g., Id.) In another example, the level of the specificmRNA produced by the target protein can be measured, e.g., using PCR. Inyet another example, Western blots can be used to measure the amount oftarget protein present. In still another embodiment, a phenotypeinfluenced by the amount of the protein can be detected. Techniques forperforming Western blots are well known in the art, see, e.g., Chen etal. J. Biol. Chem. 271:28259.

In another example, the promoter sequence of a target gene can be linkedto a reporter gene and reporter gene transcription (e.g., as describedin more detail below) can be monitored. Alternatively, oligonucleotidecompositions that do not target a promoter can be identified by fusing aportion of the target nucleic acid molecule with a reporter gene so thatthe reporter gene is transcribed. By monitoring a change in theexpression of the reporter gene in the presence of the oligonucleotidecomposition, it is possible to determine the effectiveness of theoligonucleotide composition in inhibiting the expression of the reportergene. For example, in one embodiment, an effective oligonucleotidecomposition will reduce the expression of the reporter gene. Byincrementally adjusting the concentrations and identities of theoligonucleotides in the oligonucleotide composition and monitoring theresulting change in reporter gene expression, it is possible to optimizethe oligonucleotide composition.

A “reporter gene” is a nucleic acid that expresses a detectable geneproduct, which may be RNA or protein. Detection of mRNA expression maybe accomplished by Northern blotting and detection of protein may beaccomplished by staining with antibodies specific to the protein.Preferred reporter genes produce a readily detectable product. Areporter gene may be operably linked with a regulatory DNA sequence suchthat detection of the reporter gene product provides a measure of thetranscriptional activity of the regulatory sequence. In preferredembodiments, the gene product of the reporter gene is detected by anintrinsic activity associated with that product. For instance, thereporter gene may encode a gene product that, by enzymatic activity,gives rise to a detectable signal based on color, fluorescence, orluminescence. Examples of reporter genes include, but are not limitedto, those coding for chloramphenicol acetyl transferase (CAT),luciferase, β-galactosidase and alkaline phosphatase.

One skilled in the art would readily recognize numerous reporter genessuitable for use in the present invention. These include, but are notlimited to, chloramphenicol acetyltransferase (CAT), luciferase, humangrowth hormone (hGH), and β-galactosidase. Examples of such reportergenes can be found in F. A. Ausubel et al., Eds., Current Protocols inMolecular Biology, John Wiley & Sons, New York, (1989). Any gene thatencodes a detectable product, e.g., any product having detectableenzymatic activity or against which a specific antibody can be raised,can be used as a reporter gene in the present methods.

One reporter gene system is the firefly luciferase reporter system.(Gould, S. J., and Subramani, S. 1988. Anal. Biochem., 7:404-408incorporated herein by reference). The luciferase assay is fast andsensitive. In this assay, a lysate of the test cell is prepared andcombined with ATP and the substrate luciferin. The encoded enzymeluciferase catalyzes a rapid, ATP dependent oxidation of the substrateto generate a light-emitting product. The total light output is measuredand is proportional to the amount of luciferase present over a widerange of enzyme concentrations.

CAT is another frequently used reporter gene system; a major advantageof this system is that it has been an extensively validated and iswidely accepted as a measure of promoter activity. (Gorman C. M.,Moffat, L. F., and Howard, B. H. 1982. Mol. Cell. Biol., 2:1044-1051).In this system, test cells are transfected with CAT expression vectorsand incubated with the candidate substance within 2-3 days of theinitial transfection. Thereafter, cell extracts are prepared. Theextracts are incubated with acetyl CoA and radioactive chloramphenicol.Following the incubation, acetylated chloramphenicol is separated fromnonacetylated form by thin layer chromatography. In this assay, thedegree of acetylation reflects the CAT gene activity with the particularpromoter.

Another suitable reporter gene system is based on immunologic detectionof hGH. This system is also quick and easy to use. (Selden, R.,Burke-Howie, K. Rowe, M. E., Goodman, H. M., and Moore, D. D. (1986),Mol. Cell. Biol., 6:3173-3179 incorporated herein by reference). The hGHsystem is advantageous in that the expressed hGH polypeptide is assayedin the media, rather than in a cell extract. Thus, this system does notrequire the destruction of the test cells. It will be appreciated thatthe principle of this reporter gene system is not limited to hGH butrather adapted for use with any polypeptide for which an antibody ofacceptable specificity is available or can be prepared.

Uptake of Oligonucleotides by Cells

Oligonucleotides and oligonucleotide compositions are contacted with(i.e., brought into contact with, also referred to herein asadministered or delivered to) and taken up by one or more cells. Theterm “cells” includes prokaryotic and eukaryotic cells, preferablyvertebrate cells, and, more preferably, mammalian cells. In a preferredembodiment, the oligonucleotide compositions of the invention arecontacted with human cells.

Oligonucleotide compositions of the invention can be contacted withcells in vitro or in vivo. Oligonucleotides are taken up by cells at aslow rate by endocytosis, but endocytosed oligonucleotides are generallysequestered and not available, e.g., for hybridization to a targetnucleic acid molecule. In one embodiment, cellular uptake can befacilitated by electroporation or calcium phosphate precipitation.However, these procedures are only useful for in vitro or ex vivoembodiments, are not convenient and, in some cases, are associated withcell toxicity.

In another embodiment, delivery of oligonucleotides into cells can beenhanced by suitable art recognized methods including calcium phosphate,DMSO, glycerol or dextran, electroporation, or by transfection, e.g.,using cationic, anionic, or neutral lipid compositions or liposomesusing methods known in the art (see e.g., WO 90/14074; WO 91/16024; WO91/17424; U.S. Pat. No. 4,897,355; Bergan et al. 1993. Nucleic AcidsResearch. 21:3567). Enhanced delivery of oligonucleotides can also bemediated by the use of viruses, polyamine or polycation conjugates usingcompounds such as polylysine, protamine, or N1,N12-bis(ethyl)spermine(see e.g., Bartzatt, R. et al. 1989. Biotechnol. Appl. Biochem. 11:133;Wagner E. et al. 1992. Proc. Natl. Acad. Sci. 88:4255).

Conjugating Agents

Conjugating agents bind to the oligonucleotide in a covalent manner. Inone embodiment, oligonucleotides can be derivitized or chemicallymodified by binding to a conjugating agent to facilitate cellularuptake. For example, covalent linkage of a cholesterol moiety to anoligonucleotide can improve cellular uptake by 5- to 10-fold which inturn improves DNA binding by about 10-fold (Boutorin et al., 1989, FEBSLetters 254:129-132). Conjugation of octyl, dodecyl, and octadecylresidues enhances cellular uptake by 3-, 4-, and 10-fold as compared tounmodified oligonucleotides (Vlassov et al., 1994, Biochimica etBiophysica Acta 1197:95-108). Similarly, derivatization ofoligonucleotides with poly-L-lysine can aid oligonucleotide uptake bycells (Schell, 1974, Biochem. Biophys. Acta 340:323, and Lemaitre etal., 1987, Proc. Natl. Acad. Sci. USA 84:648).

Certain protein carriers can also facilitate cellular uptake ofoligonucleotides, including, for example, serum albumin, nuclearproteins possessing signals for transport to the nucleus, and viral orbacterial proteins capable of cell membrane penetration. Therefore,protein carriers are useful when associated with or linked to theoligonucleotides. Accordingly, the present invention provides forderivatization of oligonucleotides with groups capable of facilitatingcellular uptake, including hydrocarbons and non-polar groups,cholesterol, long chain alcohols (i.e., hexanol), poly-L-lysine andproteins, as well as other aryl or steroid groups and polycations havinganalogous beneficial effects, such as phenyl or naphthyl groups,quinoline, anthracene or phenanthracene groups, fatty acids, fattyalcohols and sesquiterpenes, diterpenes and steroids. A major advantageof using conjugating agents is to increase the initial membraneinteraction that leads to a greater cellular accumulation ofoligonucleotides.

Encapsulating Agents

Encapsulating agents entrap oligonucleotides within vesicles. In anotherembodiment, an oligonucleotide may be associated with a carrier orvehicle, e.g., liposomes or micelles, although other carriers could beused, as would be appreciated by one skilled in the art. Liposomes arevesicles made of a lipid bilayer having a structure similar tobiological membranes. Such carriers are used to facilitate the cellularuptake or targeting of the oligonucleotide, or improve theoligonucleotide's pharmacokinetic or toxicologic properties.

For example, the oligonucleotides of the present invention may also beadministered encapsulated in liposomes, pharmaceutical compositionswherein the active ingredient is contained either dispersed or variouslypresent in corpuscles consisting of aqueous concentric layers adherentto lipidic layers. The oligonucleotides, depending upon solubility, maybe present both in the aqueous layer and in the lipidic layer, or inwhat is generally termed a liposomic suspension. The hydrophobic layer,generally but not exclusively, comprises phopholipids such as lecithinand sphingomyelin, steroids such as cholesterol, more or less ionicsurfactants such as diacetylphosphate, stearylamine, or phosphatidicacid, or other materials of a hydrophobic nature. The diameters of theliposomes generally range from about 15 nm to about 5 microns.

The use of liposomes as drug delivery vehicles offers severaladvantages. Liposomes increase intracellular stability, increase uptakeefficiency and improve biological activity. Liposomes are hollowspherical vesicles composed of lipids arranged in a similar fashion asthose lipids which make up the cell membrane. They have an internalaqueous space for entrapping water soluble compounds and range in sizefrom 0.05 to several microns in diameter. Several studies have shownthat liposomes can deliver nucleic acids to cells and that the nucleicacids remain biologically active. For example, a liposome deliveryvehicle originally designed as a research tool, such as Lipofectin, candeliver intact nucleic acid molecules to cells.

Specific advantages of using liposomes include the following: they arenon-toxic and biodegradable in composition; they display longcirculation half-lives; and recognition molecules can be readilyattached to their surface for targeting to tissues. Finally,cost-effective manufacture of liposome-based pharmaceuticals, either ina liquid suspension or lyophilized product, has demonstrated theviability of this technology as an acceptable drug delivery system.

Complexing Agents

Complexing agents bind to the oligonucleotide by a strong butnon-covalent attraction (e.g., an electrostatic, van der Waals,pi-stacking interaction, etc.). In one embodiment, oligonucleotides ofthe invention can be complexed with a complexing agent to increasecellular uptake of oligonucleotides. An example of a complexing agentincludes cationic lipids. Cationic lipids can be used to deliveroligonucleotides to cells.

The term “cationic lipid” includes lipids and synthetic lipids havingboth polar and non-polar domains and which are capable of beingpositively charged at or around physiological pH and which bind topolyanions, such as nucleic acids, and facilitate the delivery ofnucleic acids into cells. In general cationic lipids include saturatedand unsaturated alkyl and alicyclic ethers and esters of amines, amides,or derivatives thereof. Straight-chain and branched alkyl and alkenylgroups of cationic lipids can contain, e.g., from 1 to about 25 carbonatoms. Preferred straight chain or branched alkyl or alkene groups havesix or more carbon atoms. Alicyclic groups include cholesterol and othersteroid groups. Cationic lipids can be prepared with a variety ofcounterions (anions) including, e.g., Cl⁻, Br⁻, I⁻, F⁻, acetate,trifluoroacetate, sulfate, nitrite, and nitrate.

Examples of cationic lipids include: polyethylenimine, polyamidoamine(PAMAM) starburst dendrimers, Lipofectin (a combination of DOTMA andDOPE), Lipofectase, Lipofectamine, DOPE, Cytofectin (Gilead Sciences,Foster City, Calif.), and Eufectins (JBL, San Luis Obispo, Calif.).Cationic liposomes may comprise the following:N-[1-(2,3-dioleoloxy)-propyl]-N,N,N-trimethylammonium chloride (DOTMA),N-[1-(2,3-dioleoloxy)-propyl]-N,N,N-trimethylammonium methylsulfate(DOTAP), 3p-[N-(N′,N′-dimethylaminoethane)carbamoyl]cholesterol(DC-Chol),2,3,-dioleyloxy-N-[2(sperminecarboxamido)ethyl]-N,N-dimethyl-1-propanaminiumtrifluoroacetate (DOSPA),1,2-dimyristyloxypropyl-3-dimethy-1-hydroxyethyl ammonium bromide; anddimethyldioctadecylammonium bromide (DDAB). The cationic lipidN-(1-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA),for example, was found to increase 1000-fold the antisense effect of aphosophorothioate oligonucleotide. (Vlassov et al., 1994, Biochimica etBiophysica Acta 1197:95-108). Oligonucleotides can also be complexedwith, e.g., poly(L-lysine) or avidin and lipids may, or may not, beincluded in this mixture (e.g., steryl-poly(L-lysine).

Cationic lipids have been used in the art to deliver oligonucleotides tocells (see, e.g., U.S. Pat. Nos. 5,855,910; 5,851,548; 5,830,430;5,780,053; 5,767,099; Lewis et al. 1996. Proc. Natl. Acad. Sci. USA93:3176; Hope et al. 1998. Molecular Membrane Biology 15:1). Other lipidcompositions which can be used to facilitate uptake of the instantoligonucleotides can be used in connection with the claimed methods. Inaddition to those listed supra, other lipid compositions are also knownin the art and include, e.g., those taught in U.S. Pat. No. 4,235,871;U.S. Pat. Nos. 4,501,728; 4,837,028; 4,737,323.

In one embodiment lipid compositions can further comprise agents, e.g.,viral proteins to enhance lipid-mediated transfections ofoligonucleotides (Kamata et al. 1994. Nucl. Acids. Res. 22:536). Inanother embodiment, oligonucleotides are contacted with cells as part ofa composition comprising an oligonucleotide, a peptide, and a lipid astaught, e.g., in U.S. Pat. No. 5,736,392. Improved lipids have also beendescribed which are serum resistant (Lewis et al. 1996. Proc. Natl.Acad. Sci. 93:3176). Cationic lipids and other complexing agents act toincrease the number of oligonucleotides carried into the cell throughendocytosis.

In another embodiment N-substituted glycine oligonucleotides (peptoids)can be used to optimize uptake of oligonucleotides. Peptoids have beenused to create cationic lipid-like compounds for transfection (Murphy etal. 1998. Proc. Natl. Acad. Sci. 95:1517). Peptoids can be synthesizedusing standard methods (e.g., Zuckermann, R. N., et al. 1992. J. Am.Chem. Soc. 114:10646; Zuckermann, R. N., et al. 1992. Int. J. PeptideProtein Res. 40:497). Combinations of cationic lipids and peptoids,liptoids, can also be used to optimize uptake of the subjectoligonucleotides (Hunag et al. 1998. Chemistry and Biology. 5:345).Liptoids can be synthesized by elaborating peptoid oligonucleotides andcoupling the amino terminal submonomer to a lipid via its amino group(Hunag et al. 1998. Chemistry and Biology. 5:345).

It is known in the art that positively charged amino acids can be usedfor creating highly active cation lipids (Lewis et al. 1996. Proc. Natl.Acad. Sci. U.S.A. 93:3176). In one embodiment, a composition fordelivering oligonucleotides of the invention comprises a number ofarginine, lysine, histadine or ornithine residues linked to a lipophilicmoiety (see, e.g., U.S. Pat. No. 5,777,153).

In another, a composition for delivering oligonucleotides of theinvention comprises a peptide having from between about one to aboutfour basic residues. These basic residues can be located, e.g., on theamino terminal, C-terminal, or internal region of the peptide. Familiesof amino acid residues having similar side chains have been defined inthe art. These families include amino acids with basic side chains(e.g., lysine, arginine, histidine), acidic side chains (e.g., asparticacid, glutamic acid), uncharged polar side chains (e.g., glycine (canalso be considered non-polar), asparagine, glutamine, serine, threonine,tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine,leucine, isoleucine, proline, phenylalanine, methionine, tryptophan),β-branched side chains (e.g., threonine, valine, isoleucine) andaromatic side chains (e.g., tyrosine, phenylalanine, tryptophan,histidine). Apart from the basic amino acids, a majority or all of theother residues of the peptide can be selected from the non-basic aminoacids, e.g., amino acids other than lysine, arginine, or histidine.Preferably a preponderance of neutral amino acids with long neutral sidechains are used. For example, a peptide such as (N-term)His-Ile-Trp-Leu-Ile-Tyr-Leu-Trp-Ile-Val-(C-term) (SEQ ID NO: 1) could beused. In one embodiment such a composition can be mixed with thefusogenic lipid DOPE as is well known in the art.

In one embodiment, the cells to be contacted with an oligonucleotidecomposition are contacted with a mixture comprising the oligonucleotideand a mixture comprising a lipid, e.g., one of the lipids or lipidcompositions described supra for between about 1 and about five days. Inone embodiment, the cells are contacted with a mixture comprising alipid and the oligonucleotide for between about three days to as long asabout 30 days. In another embodiment, a mixture comprising a lipid isleft in contact with the cells for at least about five to about 20 days.In another embodiment, a mixture comprising a lipid is left in contactwith the cells for at least about seven to about 15 days.

For example, in one embodiment, an oligonucleotide composition can becontacted with cells in the presence of a lipid such as cytofectin CS orGSV(available from Glen Research; Sterling, Va.), GS3815, GS2888 forprolonged incubation periods as described herein.

In one embodiment the incubation of the cells with the mixturecomprising a lipid and an oligonucleotide composition does not reducethe viability of the cells. Preferably, after the transfection periodthe cells are substantially viable. In one embodiment, aftertransfection, the cells are between at least about 70 and at least about100 percent viable. In another embodiment, the cells are between atleast about 80 and at least about 95% viable. In yet another embodiment,the cells are between at least about 85% and at least about 90% viable.

In one embodiment, oligonucleotides are modified by attaching a peptidesequence that transports the oligonucleotide into a cell, referred toherein as a “transporting peptide.” In one embodiment, the compositionincludes an oligonucleotide which is complementary to a target nucleicacid molecule encoding the protein, and a covalently attachedtransporting peptide.

The language “transporting peptide” includes an amino acid sequence thatfacilitates the transport of an oligonucleotide into a cell. Exemplarypeptides which facilitate the transport of the moieties to which theyare linked into cells are known in the art, and include, e.g., HIV TATtranscription factor, lactoferrin, Herpes VP22 protein, and fibroblastgrowth factor 2 (Pooga et al. 1998. Nature Biotechnology. 16:857; andDerossi et al. 1998. Trends in Cell Biology. 8:84; Elliott and O'Hare.1997. Cell 88:223).

For example, in one embodiment, the transporting peptide comprises anamino acid sequence derived from the antennapedia protein. Preferably,the peptide comprises amino acids 43-58 of the antennapedia protein(Arg-Gln-Ile-Lys-Ile-Trp-Phe-Gln-Asn-Arg-Arg-Met-Lys-Trp-Lys-Lys) (SEQID NO: 2) or a portion or variant thereof that facilitates transport ofan oligonucleotide into a cell (see, e.g., WO 91/1898; Derossi et al.1998. Trends Cell Biol. 8:84). Exemplary variants are shown in Derossiet al., supra.

In one embodiment, the transporting peptide comprises an amino acidsequence derived from the transportan, galanin (1-12)-Lys-mastoparan(1-14) amide, protein. (Pooga et al. 1998. Nature Biotechnology 16:857).Preferably, the peptide comprises the amino acids of the transportanprotein shown in the sequence GWTLNSAGYLLGKINLKALAALAKKIL (SEQ ID NO: 3)or a portion or variant thereof that facilitates transport of anoligonucleotide into a cell.

In one embodiment, the transporting peptide comprises an amino acidsequence derived from the HIV TAT protein. Preferably, the peptidecomprises amino acids 37-72 of the HIV TAT protein, e.g., shown in thesequence C(Acm)FITKALGISYGRKKRRQRRRPPQC (SEQ ID NO: 4) (TAT 37-60; whereC(Acm) is Cys-acetamidomethyl) or a portion or variant thereof, e.g.,C(Acm)GRKKRRQRRRPPQC (SEQ ID NO: 5) (TAT 48-40) orC(Acm)LGISYGRKKRRQRRPPQC (SEQ ID NO: 6) (TAT 43-60) that facilitatestransport of an oligonucleotide into a cell (Vives et al. 1997. J. Biol.Chem. 272:16010). In another embodiment the peptide(G)CFITKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQ (SEQ ID NO: 7) can be used.

Portions or variants of transporting peptides can be readily tested todetermine whether they are equivalent to these peptide portions bycomparing their activity to the activity of the native peptide, e.g.,their ability to transport fluorescently labeled oligonucleotides tocells. Fragments or variants that retain the ability of the nativetransporting peptide to transport an oligonucleotide into a cell arefunctionally equivalent and can be substituted for the native peptides.

Oligonucleotides can be attached to the transporting peptide using knowntechniques (e.g., Prochiantz, A. 1996. Curr. Opin. Neurobiol. 6:629;Derossi et al. 1998. Trends Cell Biol. 8:84; Troy et al. 1996. J.Neurosci. 16:253), Vives et al. 1997. J. Biol. Chem. 272:16010). Forexample, in one embodiment, oligonucleotides bearing an activated thiolgroup are linked via that thiol group to a cysteine present in atransport peptide (e.g., to the cysteine present in the β turn betweenthe second and the third helix of the antennapedia homeodomain astaught, e.g., in Derossi et al. 1998. Trends Cell Biol. 8:84;Prochiantz. 1996. Current Opinion in Neurobiol. 6:629; Allinquant et al.1995. J. Cell Biol. 128:919). In another embodiment, a Boc-Cys-(Npys)OHgroup can be coupled to the transport peptide as the last (N-terminal)amino acid and an oligonucleotide bearing an SH group can be coupled tothe peptide (Troy et al. 1996. J. Neurosci. 16:253).

In one embodiment, a linking group can be attached to a nucleomonomerand the transporting peptide can be covalently attached to the linker.In one embodiment, a linker can function as both an attachment site fora transporting peptide and can provide stability against nucleases.Examples of suitable linkers include substituted or unsubstituted C₁-C₂₀alkyl chains, C₁-C₂₀ alkenyl chains, C₁-C₂₀ alkynyl chains, peptides,and heteroatoms (e.g., S, O, NH, etc.). Other exemplary linkers includebifunctional crosslinking agents such assulfosuccinimidyl-4-(maleimidophenyl)-butyrate (SMPB) (see, e.g., Smithet al. Biochem J 1991.276: 417-2).

In one embodiment, oligonucleotides of the invention are synthesized asmolecular conjugates which utilize receptor-mediated endocytoticmechanisms for delivering genes into cells (see, e.g., Bunnell et al.1992. Somatic Cell and Molecular Genetics. 18:559 and the referencescited therein).

Targeting Agents

The delivery of oligonucleotides can also be improved by targeting theoligonucleotides to a cellular receptor. The targeting moieties can beconjugated to the oligonucleotides or attached to a carrier group (i.e.,poly(L-lysine) or liposomes) linked to the oligonucleotides. This methodis well suited to cells that display specific receptor-mediatedendocytosis.

For instance, oligonucleotide conjugates to 6-phosphomannosylatedproteins are internalized 20-fold more efficiently by cells expressingmannose 6-phosphate specific receptors than free oligonucleotides. Theoligonucleotides may also be coupled to a ligand for a cellular receptorusing a biodegradable linker. In another example, the delivery constructis mannosylated streptavidin which forms a tight complex withbiotinylated oligonucleotides. Mannosylated streptavidin was found toincrease 20-fold the internalization of biotinylated oligonucleotides.(Vlassov et al. 1994. Biochimica et Biophysica Acta 1197:95-108).

In addition specific ligands can be conjugated to the polylysinecomponent of polylysine-based delivery systems. For example,transferrin-polylysine, adenovirus-polylysine, and influenza virushemagglutinin HA-2 N-terminal fusogenic peptides-polylysine conjugatesgreatly enhance receptor-mediated DNA delivery in eucaryotic cells.Mannosylated glycoprotein conjugated to poly(L-lysine) in aveolarmacrophages has been employed to enhance the cellular uptake ofoligonucleotides. Liang et al. 1999. Pharmazie 54:559-566.

Because malignant cells have an increased need for essential nutrientssuch as folic acid and transferrin, these nutrients can be used totarget oligonucleotides to cancerous cells. For example, when folic acidis linked to poly(L-lysine) enhanced oligonucleotide uptake is seen inpromyelocytic leukaemia (HL-60) cells and human melanoma (M-14) cells.Ginobbi et al. 1997. Anticancer Res. 17:29. In another example,liposomes coated with maleylated bovine serum albumin, folic acid, orferric protoporphyrin IX, show enhanced cellular uptake ofoligonucleotides in murine macrophages, KB cells, and 2.2.15 humanhepatoma cells. Liang et al. 1999. Pharmazie 54:559-566.

Liposomes are naturally targeted to the liver, spleen, andreticuloendothelial system. By coupling liposomes to various ligandssuch as antibodies are protein A, they can be targeted to specific cellpopulations. For example, protein A-bearing liposomes may be pretreatedwith H-2K specific antibodies which are targeted to the mouse majorhistocompatibility complex-encoded H-2K protein expressed on L cells.(Vlassov et al. 1994. Biochimica et Biophysica Acta 1197:95-108).

Assays of Oligonucleotide Stability

Preferably, the oligonucleotides of the invention are stabilized, i.e.,substantially resistant to endonuclease and exonuclease degradation. Anoligonucleotide is defined as being substantially resistant to nucleaseswhen it is at least about 3-fold more resistant to attack by anendogenous cellular nuclease, and is highly nuclease resistant when itis at least about 6-fold more resistant than a corresponding, unmodifiedoligonucleotide. This can be demonstrated by showing that theoligonucleotides of the invention are substantially resist nucleasesusing techniques which are known in the art.

One way in which substantial stability can be demonstrated is showingthat the oligonucleotides of the invention function when delivered to acell, e.g., that they reduce transcription or translation of targetnucleic acid molecules, e.g., by measuring protein levels or bymeasuring cleavage of mRNA. Assays which measure the stability of targetRNA can be performed at about 24 hours post-transfection (e.g., usingNorthern blot techniques, RNase Protection Assays, or QC-PCR assays asknown in the art). Alternatively, levels of the target protein can bemeasured. Preferably, in addition to testing the RNA or protein levelsof interest, the RNA or protein levels of a control, non-targeted genewill be measured (e.g., actin, or preferably a control with sequencesimilarity to the target) as a specificity control. RNA or proteinmeasurements can be made using any art-recognized technique. Preferably,measurements will be made beginning at about 16-24 hours posttransfection. (M. Y. Chiang, et al. 1991. J Biol Chem. 266:18162-71; T.Fisher, et al. 1993. Nucleic Acids Research. 21 3857).

The ability of an oligonucleotide composition of the invention toinhibit protein synthesis can be measured using techniques which areknown in the art, for example, by detecting an inhibition in genetranscription or protein synthesis. For example, Nuclease S1 mapping canbe performed. In another example, Northern blot analysis can be used tomeasure the presence of RNA encoding a particular protein. For example,total RNA can be prepared over a cesium chloride cushion (see, e.g.,Ausebel et al., 1987. Current Protocols in Molecular Biology (Greene &Wiley, New York)). Northern blots can then be made using the RNA andprobed (see, e.g., Id.). In another example, the level of the specificmRNA produced by the target protein can be measured, e.g., using PCR. Inyet another example, Western blots can be used to measure the amount oftarget protein present. In still another embodiment, a phenotypeinfluenced by the amount of the protein can be detected. Techniques forperforming Western blots are well known in the art, see, e.g., Chen etal. J. Biol. Chem. 271:28259.

In another example, the promoter sequence of a target gene can be linkedto a reporter gene and reporter gene transcription (e.g., as describedin more detail below) can be monitored. Alternatively, oligonucleotidecompositions that do not target a promoter can be identified by fusing aportion of the target nucleic acid molecule with a reporter gene so thatthe reporter gene is transcribed. By monitoring a change in theexpression of the reporter gene in the presence of the oligonucleotidecomposition, it is possible to determine the effectiveness of theoligonucleotide composition in inhibiting the expression of the reportergene. For example, in one embodiment, an effective oligonucleotidecomposition will reduce the expression of the reporter gene.

A “reporter gene” is a nucleic acid that expresses a detectable geneproduct, which may be RNA or protein. Detection of mRNA expression maybe accomplished by Northern blotting and detection of protein may beaccomplished by staining with antibodies specific to the protein.Preferred reporter genes produce a readily detectable product. Areporter gene may be operably linked with a regulatory DNA sequence suchthat detection of the reporter gene product provides a measure of thetranscriptional activity of the regulatory sequence. In preferredembodiments, the gene product of the reporter gene is detected by anintrinsic activity associated with that product. For instance, thereporter gene may encode a gene product that, by enzymatic activity,gives rise to a detectable signal based on color, fluorescence, orluminescence. Examples of reporter genes include, but are not limitedto, those coding for chloramphenicol acetyl transferase (CAT),luciferase, β-galactosidase, and alkaline phosphatase.

One skilled in the art would readily recognize numerous reporter genessuitable for use in the present invention. These include, but are notlimited to, chloramphenicol acetyltransferase (CAT), luciferase, humangrowth hormone (hGH), and β-galactosidase. Examples of such reportergenes can be found in F. A. Ausubel et al., Eds., Current Protocols inMolecular Biology, John Wiley & Sons, New York, (1989). Any gene thatencodes a detectable product, e.g., any product having detectableenzymatic activity or against which a specific antibody can be raised,can be used as a reporter gene in the present methods.

One reporter gene system is the firefly luciferase reporter system.(Gould, S. J., and Subramani, S. 1988. Anal. Biochem., 7:404-408incorporated herein by reference). The luciferase assay is fast andsensitive. In this assay, a lysate of the test cell is prepared andcombined with ATP and the substrate luciferin. The encoded enzymeluciferase catalyzes a rapid, ATP dependent oxidation of the substrateto generate a light-emitting product. The total light output is measuredand is proportional to the amount of luciferase present over a widerange of enzyme concentrations.

CAT is another frequently used reporter gene system; a major advantageof this system is that it has been an extensively validated and iswidely accepted as a measure of promoter activity. (Gorman C. M.,Moffat, L. F., and Howard, B. H. 1982. Mol. Cell. Biol., 2:1044-1051).In this system, test cells are transfected with CAT expression vectorsand incubated with the candidate substance within 2-3 days of theinitial transfection. Thereafter, cell extracts are prepared. Theextracts are incubated with acetyl CoA and radioactive chloramphenicol.Following the incubation, acetylated chloramphenicol is separated fromnonacetylated form by thin layer chromatography. In this assay, thedegree of acetylation reflects the CAT gene activity with the particularpromoter.

Another suitable reporter gene system is based on immunologic detectionof hGH. This system is also quick and easy to use. (Selden, R.,Burke-Howie, K. Rowe, M. E., Goodman, H. M., and Moore, D. D. (1986),Mol. Cell. Biol., 6:3173-3179 incorporated herein by reference). The hGHsystem is advantageous in that the expressed hGH polypeptide is assayedin the media, rather than in a cell extract. Thus, this system does notrequire the destruction of the test cells. It will be appreciated thatthe principle of this reporter gene system is not limited to hGH butrather adapted for use with any polypeptide for which an antibody ofacceptable specificity is available or can be prepared.

Oligonucleotide Synthesis

Oligonucleotides of the invention can be synthesized by any methodsknown in the art, e.g., using enzymatic synthesis and chemicalsynthesis. The oligonucleotides can be synthesized in vitro (e.g., usingenzymatic synthesis and chemical synthesis) or in vivo (usingrecombinant DNA technology well known in the art.

In a preferred embodiment, chemical synthesis is used. Chemicalsynthesis of linear oligonucleotides is well known in the art and can beachieved by solution or solid phase techniques. Preferably, synthesis isby solid phase methods. Oligonucleotides can be made by any of severaldifferent synthetic procedures including the phosphoramidite, phosphitetriester, H-phosphonate, and phosphotriester methods, typically byautomated synthesis methods.

Oligonucleotide synthesis protocols are well known in the art and can befound, e.g., in U.S. Pat. No. 5,830,653; WO 98/13526; Stec et al. 1984.J. Am. Chem. Soc. 106:6077; Stec et al. 1985. J Org. Chem. 50:3908; Stecet al. J. Chromatog. 1985. 326:263; LaPlanche et al. 1986. Nuc. Acid.Res. 1986. 14:9081; Fasman G. D., 1989. Practical Handbook ofBiochemistry and Molecular Biology. 1989. CRC Press, Boca Raton, Fla.;Lamone. 1993. Biochem. Soc. Trans. 21:1; U.S. Pat. No. 5,013,830; U.S.Pat. No. 5,214,135; U.S. Pat. No. 5,525,719; Kawasaki et al. 1993. JMed. Chem. 36:831; WO 92/03568; U.S. Pat. No. 5,276,019; U.S. Pat. No.5,264,423.

The synthesis method selected can depend on the length of the desiredoligonucleotide and such choice is within the skill of the ordinaryartisan. For example, the phosphoramidite and phosphite triester methodproduce oligonucleotides having 175 or more nucleotides while theH-phosphonate method works well for oligonucleotides of less than 100nucleotides. If modified bases are incorporated into theoligonucleotide, and particularly if modified phosphodiester linkagesare used, then the synthetic procedures are altered as needed accordingto known procedures. In this regard, Uhlmann et al. (1990, ChemicalReviews 90:543-584) provide references and outline procedures for makingoligonucleotides with modified bases and modified phosphodiesterlinkages. Other exemplary methods for making oligonucleotides are taughtin Sonveaux. 1994. “Protecting Groups in Oligonucleotide Synthesis”;Agrawal. Methods in Molecular Biology 26:1. Exemplary synthesis methodsare also taught in “Oligonucleotide Synthesis—A Practical Approach”(Gait, M. J. IRL Press at Oxford University Press. 1984). Moreover,linear oligonucleotides of defined sequence can be purchasedcommercially.

The oligonucleotides may be purified by polyacrylamide gelelectrophoresis, or by any of a number of chromatographic methods,including gel chromatography and high pressure liquid chromatography. Toconfirm a nucleotide sequence, oligonucleotides may be subjected to DNAsequencing by any of the known procedures, including Maxam and Gilbertsequencing, Sanger sequencing, capillary electrophoresis sequencing thewandering spot sequencing procedure or by using selective chemicaldegradation of oligonucleotides bound to Hybond paper. Sequences ofshort oligonucleotides can also be analyzed by laser desorption massspectroscopy or by fast atom bombardment (McNeal, et al., 1982, J Am.Chem. Soc. 104:976; Viari, et al., 1987, Biomed. Environ. Mass Spectrom.14:83; Grotjahn et al., 1982, Nuc. Acid Res. 10:4671). Sequencingmethods are also available for RNA oligonucleotides.

The quality of oligonucleotides synthesized can be verified by testingthe oligonucleotide by capillary electrophoresis and denaturing stronganion HPLC (SAX-HPLC) using, e.g., the method of Bergot and Egan. 1992.J Chrom. 599:35.

Other exemplary synthesis techniques are well known in the art (see,e.g., Sambrook et al., Molecular Cloning: a Laboratory Manual, SecondEdition (1989); DNA Cloning, Volumes I and II (DN Glover Ed. 1985);Oligonucleotide Synthesis (M J Gait Ed, 1984; Nucleic Acid Hybridisation(B D Hames and S J Higgins eds. 1984); A Practical Guide to MolecularCloning (1984); or the series, Methods in Enzymology (Academic Press,Inc.)).

Uses of Oligonucleotides

This invention also features methods of inhibiting expression of aprotein in a cell including contacting the cell with one of theabove-described oligonucleotide compositions.

The oligonucleotides of the invention can be used in a variety of invitro and in vivo situations to specifically inhibit protein expression.The instant methods and compositions are suitable for both in vitro andin vivo use.

In one embodiment, the oligonucleotides of the invention can be used toinhibit gene function in vitro in a method for identifying the functionsof genes. In this manner, the transcription of genes that areidentified, but for which no function has yet been shown, can beinhibited to thereby determine how the phenotype of a cell is changedwhen the gene is not transcribed. Such methods are useful for thevalidation of genes as targets for clinical treatment, e.g., witholigonucleotides or with other therapies.

To determine the effect of a composition of the invention, a variety ofend points can be used. In addition to the assays described previouslyherein, for example, nucleic acid probes (e.g., in the form of arrays)can be used to evaluate transcription patterns produced by cells. Probescan also be used detect peptides, proteins, or protein domains, e.g.,antibodies can be used to detect the expression of a particular protein.In yet another embodiment, the function of a protein (e.g., enzymaticactivity) can be measured. In yet another embodiment, the phenotype of acell can be evaluated to determine whether or not a target protein isexpressed. For example, the ability of a composition to affect aphenotype of a cell that is associated with cancer can be tested.

In one embodiment, one or more additional agents (e.g., activatingagents, inducing agents, proliferation enhancing agents, tumorpromoters) can be added to the cells.

In another embodiment, the compositions of the invention can be used tomonitor biochemical reactions such as, e.g., interactions of proteins,nucleic acids, small molecules, or the like--for example the efficiencyor specificity of interactions between antigens and antibodies; or ofreceptors (such as purified receptors or receptors bound to cellmembranes) and their ligands, agonists or antagonists; or of enzymes(such as proteases or kinases) and their substrates, or increases ordecreases in the amount of substrate converted to a product; as well asmany others. Such biochemical assays can be used to characterizeproperties of the probe or target, or as the basis of a screening assay.For example, to screen samples for the presence of particular proteases(e.g., proteases involved in blood clotting such as proteases Xa andVIIa), the samples can be assayed, for example using probes which arefluorogenic substrates specific for each protease of interest. If atarget protease binds to and cleaves a substrate, the substrate willfluoresce, usually as a result, e.g., of cleavage and separation betweentwo energy transfer pairs, and the signal can be detected. In anotherexample, to screen samples for the presence of a particular kinase(s)(e.g., a tyrosine kinase), samples containing one or more kinases ofinterest can be assayed, e.g., using probes are peptides which can beselectively phosphorylated by one of the kinases of interest. Usingart-recognized, routinely determinable conditions, samples can beincubated with an array of substrates, in an appropriate buffer and withthe necessary cofactors, for an empirically determined period of time.If necessary, reactions can be stopped, e.g., by washing and thephosphorylated substrates can be detected by, for example, incubatingthem with detectable reagents such as, e.g., fluorescein-labeledanti-phosphotyrosine or anti-phosphoserine antibodies and the signal canbe detected.

In another embodiment, the compositions of the invention can be used toscreen for agents which modulate a pattern of gene expression. Arrays ofoligonucleotides can be used, for example, to identify mRNA specieswhose pattern of expression from a set of genes is correlated with aparticular physiological state or developmental stage, or with a diseasecondition (“correlative” genes, RNAs, or expression patterns). By theterms “correlate” or “correlative,” it is meant that the synthesispattern of RNA is associated with the physiological condition of a cell,but not necessarily that the expression of a given RNA is responsiblefor or is causative of a particular physiological state. For example, asmall subset of mRNAs can be identified which are modulated (e.g.,upregulated or downregulated) in cells which serve as a model for aparticular disease state. This altered pattern of expression as comparedto that in a normal cell, which does not exhibit a pathologicalphenotype, can serve as an indicator of the disease state (“indicator”or “correlative” genes, RNAs, or expression patterns).

The invention also relates to a selecting oligonucleotides for themethods described herein in which in which many oligomers are screened(e.g., from about 10-20 to significantly greater numbers as may be foundin a combinatorial library), after which the more efficacious oligomersare chosen and combined to produce a composition of the invention. Thus,inhibition of greater than 95%, 90%, 85%, 80%, 70%, or 60% may beachieved.

Compositions which modulate the chosen indicator expression pattern(e.g., compared to control compositions comprising, for exampleoligonucleotides which comprise a nucleotide sequence which is thereverse of the oligonucleotide, or which contains mismatch bases) canindicate that a particular target gene is a potential target fortherapeutic intervention. Moreover, such compositions may be useful astherapeutic agents to modulate expression patters of cells in an invitro expression system or in in vivo therapy. As used herein,“modulate” means to cause to increase or decrease the amount or activityof a molecule or the like which is involved in a measurable reaction. Inone embodiment, a series of cells (e.g., from a disease model) can becontacted with a series of agents (e.g., for a period of time rangingfrom about 10 minutes to about 48 hours or more) and, using routine,art-recognized methods (e.g., commercially available kits), total RNA ormRNA extracts can be made. If it is desired to amplify the amount ofRNA, standard procedures such as RT-PCR amplification can be used (see,e.g., Innis et al. eds., (1996) PCR Protocols: A Guide to Methods inAmplification, Academic Press, New York). The extracts (or amplifiedproducts from them) can be allowed to contact (e.g., incubate with)probes for appropriate indicator RNAs, and those agents which areassociated with a change in the indicator expression pattern can beidentified.

Similarly, agents can be identified which modulate expression patternsassociated with particular physiological states or developmental stages.Such agents can be man-made or naturally-occurring substances, includingenvironmental factors such as substances involved in embryonicdevelopment or in regulating physiological reactions.

In one embodiment, the methods described herein can be performed in a“high throughput” manner, in which a large number of target genes (e.g.,as many as about 1000 or more, depending on the particular format used)are assayed rapidly and concurrently. Further, many assay formats (e.g.,plates or surfaces) can be processed at one time. For example, becausethe oligonucleotides of the invention do not need to be testedindividually before incorporating them into a composition, they can bereadily synthesized and large numbers of target genes can be tested atone time. For example, a large number of samples, each comprising abiological sample containing a target nucleic acid molecule (e.g., acell) and a composition of the invention can be added to separateregions of an assay format and assays can be performed on each of thesamples.

Administration of Oligonucleotide Compositions

The optimal course of administration or delivery of the oligonucleotidesmay vary depending upon the desired result and/ or on the subject to betreated. As used herein “administration” refers to contacting cells witholigonucleotides and can be performed in vitro or in vivo. The dosage ofoligonucleotides may be adjusted to optimally reduce expression of aprotein translated from a target nucleic acid molecule, e.g., asmeasured by a readout of RNA stability or by a therapeutic response,without undue experimentation.

For example, expression of the protein encoded by the nucleic acidtarget can be measured to determine whether or not the dosage regimenneeds to be adjusted accordingly. In addition, an increase or decreasein RNA or protein levels in a cell or produced by a cell can be measuredusing any art recognized technique. By determining whether transcriptionhas been decreased, the effectiveness of the oligonucleotide in inducingthe cleavage of a target RNA can be determined.

Any of the above-described oligonucleotide compositions can be usedalone or in conjunction with a pharmaceutically acceptable carrier. Asused herein, “pharmaceutically acceptable carrier” includes appropriatesolvents, dispersion media, coatings, antibacterial and antifungalagents, isotonic and absorption delaying agents, and the like. The useof such media and agents for pharmaceutical active substances is wellknown in the art. Except insofar as any conventional media or agent isincompatible with the active ingredient, it can be used in thetherapeutic compositions. Supplementary active ingredients can also beincorporated into the compositions.

Oligonucleotides may be incorporated into liposomes or liposomesmodified with polyethylene glycol or admixed with cationic lipids forparenteral administration. Incorporation of additional substances intothe liposome, for example, antibodies reactive against membrane proteinsfound on specific target cells, can help target the oligonucleotides tospecific cell types.

Moreover, the present invention provides for administering the subjectoligonucleotides with an osmotic pump providing continuous infusion ofsuch oligonucleotides, for example, as described in Rataiczak, et al.(1992 Proc. Natl. Acad. Sci. USA 89:11823-11827). Such osmotic pumps arecommercially available, e.g., from Alzet Inc. (Palo Alto, Calif.).Topical administration and parenteral administration in a cationic lipidcarrier are preferred.

With respect to in vivo applications, the formulations of the presentinvention can be administered to a patient in a variety of forms adaptedto the chosen route of administration, e.g., parenterally, orally, orintraperitoneally. Parenteral administration, which is preferred,includes administration by the following routes: intravenous;intramuscular; interstitially; intraarterially; subcutaneous; intraocular; intrasynovial; trans epithelial, including transdermal;pulmonary via inhalation; ophthalmic; sublingual and buccal; topically,including ophthalmic; dermal; ocular; rectal; and nasal inhalation viainsufflation.

Pharmaceutical preparations for parenteral administration includeaqueous solutions of the active compounds in water-soluble orwater-dispersible form. In addition, suspensions of the active compoundsas appropriate oily injection suspensions may be administered. Suitablelipophilic solvents or vehicles include fatty oils, for example, sesameoil, or synthetic fatty acid esters, for example, ethyl oleate ortriglycerides. Aqueous injection suspensions may contain substanceswhich increase the viscosity of the suspension include, for example,sodium carboxymethyl cellulose, sorbitol, or dextran, optionally, thesuspension may also contain stabilizers. The oligonucleotides of theinvention can be formulated in liquid solutions, preferably inphysiologically compatible buffers such as Hank's solution or Ringer'ssolution. In addition, the oligonucleotides may be formulated in solidform and redissolved or suspended immediately prior to use. Lyophilizedforms are also included in the invention.

Pharmaceutical preparations for topical administration includetransdermal patches, ointments, lotions, creams, gels, drops, sprays,suppositories, liquids and powders. In addition, conventionalpharmaceutical carriers, aqueous, powder or oily bases, or thickenersmay be used in pharmaceutical preparations for topical administration.

Pharmaceutical preparations for oral administration include powders orgranules, suspensions or solutions in water or non-aqueous media,capsules, sachets or tablets. In addition, thickeners, flavoring agents,diluents, emulsifiers, dispersing aids, or binders may be used inpharmaceutical preparations for oral administration.

For transmucosal or transdermal administration, penetrants appropriateto the barrier to be permeated are used in the formulation. Suchpenetrants are known in the art, and include, for example, fortransmucosal administration bile salts and fusidic acid derivatives, anddetergents. Transmucosal administration may be through nasal sprays orusing suppositories. For oral administration, the oligonucleotides areformulated into conventional oral administration forms such as capsules,tablets, and tonics. For topical administration, the oligonucleotides ofthe invention are formulated into ointments, salves, gels, or creams asknown in the art.

Drug delivery vehicles can be chosen e.g., for in vitro, for systemic,or for topical administration. These vehicles can be designed to serveas a slow release reservoir or to deliver their contents directly to thetarget cell. An advantage of using some direct delivery drug vehicles isthat multiple molecules are delivered per uptake. Such vehicles havebeen shown to increase the circulation half-life of drugs that wouldotherwise be rapidly cleared from the blood stream. Some examples ofsuch specialized drug delivery vehicles which fall into this categoryare liposomes, hydrogels, cyclodextrins, biodegradable nanocapsules, andbioadhesive microspheres.

The described oligonucleotides may be administered systemically to asubject. Systemic absorption refers to the entry of drugs into the bloodstream followed by distribution throughout the entire body.Administration routes which lead to systemic absorption include:intravenous, subcutaneous, intraperitoneal, and intranasal. Each ofthese administration routes delivers the oligonucleotide to accessiblediseased cells. Following subcutaneous administration, the therapeuticagent drains into local lymph nodes and proceeds through the lymphaticnetwork into the circulation. The rate of entry into the circulation hasbeen shown to be a function of molecular weight or size. The use of aliposome or other drug carrier localizes the oligonucleotide at thelymph node. The oligonucleotide can be modified to diffuse into thecell, or the liposome can directly participate in the delivery of eitherthe unmodified or modified oligonucleotide into the cell.

The chosen method of delivery will result in entry into cells. Preferreddelivery methods include liposomes (10-400 nm), hydrogels,controlled-release polymers, and other pharmaceutically applicablevehicles, and microinjection or electroporation (for ex vivotreatments).

The pharmaceutical preparations of the present invention may be preparedand formulated as emulsions. Emulsions are usually heterogenous systemsof one liquid dispersed in another in the form of droplets usuallyexceeding 0.1 μm in diameter.

The emulsions of the present invention may contain excipients such asemulsifiers, stabilizers, dyes, fats, oils, waxes, fatty acids, fattyalcohols, fatty esters, humectants, hydrophilic colloids, preservatives,and anti-oxidants may also be present in emulsions as needed. Theseexcipients may be present as a solution in either the aqueous phase,oily phase or itself as a separate phase.

Examples of naturally occurring emulsifiers that may be used in emulsionformulations of the present invention include lanolin, beeswax,phosphatides, lecithin and acacia. Finely divided solids have also beenused as good emulsifiers especially in combination with surfactants andin viscous preparations. Examples of finely divided solids that may beused as emulsifiers include polar inorganic solids, such as heavy metalhydroxides, nonswelling clays such as bentonite, attapulgite, hectorite,kaolin, montmorillonite, colloidal aluminum silicate and colloidalmagnesium aluminum silicate, pigments and nonpolar solids such as carbonor glyceryl tristearate.

Examples of preservatives that may be included in the emulsionformulations include methyl paraben, propyl paraben, quaternary ammoniumsalts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boricacid. Examples of antioxidants that may be included in the emulsionformulations include free radical scavengers such as tocopherols, alkylgallates, butylated hydroxyanisole, butylated hydroxytoluene, orreducing agents such as ascorbic acid and sodium metabisulfite, andantioxidant synergists such as citric acid, tartaric acid, and lecithin.

In one embodiment, the compositions of oligonucleotides are formulatedas microemulsions. A microemulsion is a system of water, oil andamphiphile which is a single optically isotropic and thermodynamicallystable liquid solution. Typically microemulsions are prepared by firstdispersing an oil in an aqueous surfactant solution and then adding asufficient amount of a 4th component, generally an intermediatechain-length alcohol to form a transparent system.

Surfactants that may be used in the preparation of microemulsionsinclude, but are not limited to, ionic surfactants, non-ionicsurfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fattyacid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate(MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate(PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate(MO750), decaglycerol sequioleate (S0750), decaglycerol decaoleate(DA0750), alone or in combination with cosurfactants. The cosurfactant,usually a short-chain alcohol such as ethanol, 1-propanol, and1-butanol, serves to increase the interfacial fluidity by penetratinginto the surfactant film and consequently creating a disordered filmbecause of the void space generated among surfactant molecules.

Microemulsions may, however, be prepared without the use ofcosurfactants and alcohol-free self-emulsifying microemulsion systemsare known in the art. The aqueous phase may typically be, but is notlimited to, water, an aqueous solution of the drug, glycerol, PEG300,PEG400, polyglycerols, propylene glycols, and derivatives of ethyleneglycol. The oil phase may include, but is not limited to, materials suchas Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain(C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fattyacid esters, fatty alcohols, polyglycolized glycerides, saturatedpolyglycolized C8-C10 glycerides, vegetable oils and silicone oil.

Microemulsions are particularly of interest from the standpoint of drugsolubilization and the enhanced absorption of drugs. Lipid basedmicroemulsions (both oil/water and water/oil) have been proposed toenhance the oral bioavailability of drugs.

Microemulsions offer improved drug solubilization, protection of drugfrom enzymatic hydrolysis, possible enhancement of drug absorption dueto surfactant-induced alterations in membrane fluidity and permeability,ease of preparation, ease of oral administration over solid dosageforms, improved clinical potency, and decreased toxicity (Constantinideset al., Pharmaceutical Research, 1994, 11:1385; Ho et al., J. Pharm.Sci., 1996, 85:138-143). Microemulsions have also been effective in thetransdermal delivery of active components in both cosmetic andpharmaceutical applications. It is expected that the microemulsioncompositions and formulations of the present invention will facilitatethe increased systemic absorption of oligonucleotides from thegastrointestinal tract, as well as improve the local cellular uptake ofoligonucleotides within the gastrointestinal tract, vagina, buccalcavity and other areas of administration.

In an embodiment, the present invention employs various penetrationenhancers to effect the efficient delivery of nucleic acids,particularly oligonucleotides, to the skin of animals. Evennon-lipophilic drugs may cross cell membranes if the membrane to becrossed is treated with a penetration enhancer. In addition toincreasing the diffusion of non-lipophilic drugs across cell membranes,penetration enhancers also act to enhance the permeability of lipophilicdrugs.

Five categories of penetration enhancers that may be used in the presentinvention include: surfactants, fatty acids, bile salts, chelatingagents, and non-chelating non-surfactants Other agents may be utilizedto enhance the penetration of the administered oligonucleotides include:glycols such as ethylene glycol and propylene glycol, pyrrols such as2-15 pyrrol, azones, and terpenes such as limonene and menthone.

The oligonucleotides, especially in lipid formulations, can also beadministered by coating a medical device, for example, a catheter, suchas an angioplasty balloon catheter, with a cationic lipid formulation.Coating may be achieved, for example, by dipping the medical device intoa lipid formulation or a mixture of a lipid formulation and a suitablesolvent, for example, an aqueous-based buffer, an aqueous solvent,ethanol, methylene chloride, chloroform and the like. An amount of theformulation will naturally adhere to the surface of the device which issubsequently administered to a patient, as appropriate. Alternatively, alyophilized mixture of a lipid formulation may be specifically bound tothe surface of the device. Such binding techniques are described, forexample, in K. Ishihara et al., Journal of Biomedical MaterialsResearch, Vol. 27, pp. 1309-1314 (1993), the disclosures of which areincorporated herein by reference in their entirety.

The useful dosage to be administered and the particular mode ofadministration will vary depending upon such factors as the cell type,or for in vivo use, the age, weight and the particular animal and regionthereof to be treated, the particular oligonucleotide and deliverymethod used, the therapeutic or diagnostic use contemplated, and theform of the formulation, for example, suspension, emulsion, micelle orliposome, as will be readily apparent to those skilled in the art.Typically, dosage is administered at lower levels and increased untilthe desired effect is achieved. When lipids are used to deliver theoligonucleotides, the amount of lipid compound that is administered canvary and generally depends upon the amount of oligonucleotide agentbeing administered. For example, the weight ratio of lipid compound tooligonucleotide agent is preferably from about 1:1 to about 15:1, with aweight ratio of about 5:1 to about 10:1 being more preferred. Generally,the amount of cationic lipid compound which is administered will varyfrom between about 0.1 milligram (mg) to about 1 gram (g). By way ofgeneral guidance, typically between about 0.1 mg and about 10 mg of theparticular oligonucleotide agent, and about 1 mg to about 100 mg of thelipid compositions, each per kilogram of patient body weight, isadministered, although higher and lower amounts can be used.

The agents of the invention are administered to subjects or contactedwith cells in a biologically compatible form suitable for pharmaceuticaladministration. By “biologically compatible form suitable foradministration” is meant that the oligonucleotide is administered in aform in which any toxic effects are outweighed by the therapeuticeffects of the oligonucleotide. In one embodiment, oligonucleotides canbe administered to subjects. Examples of subjects include mammals, e.g.,humans, cows, pigs, horses, dogs, cats, mice, rats, and transgenicnon-human animals.

Administration of an active amount of an oligonucleotide of the presentinvention is defined as an amount effective, at dosages and for periodsof time necessary to achieve the desired result. For example, an activeamount of an oligonucleotide may vary according to factors such as thetype of cell, the oligonucleotide used, and for in vivo uses the diseasestate, age, sex, and weight of the individual, and the ability of theoligonucleotide to elicit a desired response in the individual.Establishment of therapeutic levels of oligonucleotides within the cellis dependent upon the rates of uptake and efflux or degradation.Decreasing the degree of degradation prolongs the intracellularhalf-life of the oligonucleotide. Thus, chemically-modifiedoligonucleotides, e.g., with modification of the phosphate backbone, mayrequire different dosing.

The exact dosage of an oligonucleotide and number of doses administeredwill depend upon the data generated experimentally and in clinicaltrials. Several factors such as the desired effect, the deliveryvehicle, disease indication, and the route of administration, willaffect the dosage. Dosages can be readily determined by one of ordinaryskill in the art and formulated into the subject pharmaceuticalcompositions. Preferably, the duration of treatment will extend at leastthrough the course of the disease symptoms.

Dosage regima may be adjusted to provide the optimum therapeuticresponse. For example, the oligonucleotide may be repeatedlyadministered, e.g., several doses may be administered daily or the dosemay be proportionally reduced as indicated by the exigencies of thetherapeutic situation. One of ordinary skill in the art will readily beable to determine appropriate doses and schedules of administration ofthe subject oligonucleotides, whether the oligonucleotides are to beadministered to cells or to subjects.

Treatment of Diseases or Disorders

By inhibiting the expression of a gene, the oligonucleotide compositionsof the present invention can be used to treat any disease involving theexpression of a protein. Examples of diseases that can be treated byoligonucleotide compositions include: cancer, retinopathies, autoimmunediseases, inflammatory diseases (e.g., ICAM-1 related disorders,Psoriasis, Ulcerative Colitus, Crohn's disease), viral diseases (e.g.,HIV, Hepatitis C), and cardiovascular diseases.

In one embodiment, in vitro treatment of cells with oligonucleotides canbe used for ex vivo therapy of cells removed from a subject (e.g., fortreatment of leukemia or viral infection) or for treatment of cellswhich did not originate in the subject, but are to be administered tothe subject (e.g., to eliminate transplantation antigen expression oncells to be transplanted into a subject). In addition, in vitrotreatment of cells can be used in non-therapeutic settings, e.g., toevaluate gene function, to study gene regulation and protein synthesisor to evaluate improvements made to oligonucleotides designed tomodulate gene expression or protein synthesis. In vivo treatment ofcells can be useful in certain clinical settings where it is desirableto inhibit the expression of a protein. There are numerous medicalconditions for which antisense therapy is reported to be suitable (seee.g., U.S. Pat. No. 5,830,653) as well as respiratory syncytial virusinfection (WO 95/22553) influenza virus (WO 94/23028), and malignancies(WO 94/08003). Other examples of clinical uses of antisenseoligonucleotides are reviewed, e.g., in Glaser. 1996. GeneticEngineering News 16:1. Exemplary targets for cleavage byoligonucleotides include e.g., protein kinase Ca, ICAM-1, c-raf kinase,p53, c-myb, and the bcr/abl fusion gene found in chronic myelogenousleukemia.

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques of cell biology, cell culture,molecular biology, microbiology, recombinant DNA, and immunology, whichare within the skill of the art. Such techniques are explained fully inthe literature. See, for example, Molecular Cloning A Laboratory Manual,2nd Ed., ed. by Sambrook, J. et al. (Cold Spring Harbor Laboratory Press(1989)); Short Protocols in Molecular Biology, 3rd Ed., ed. by Ausubel,F. et al. (Wiley, N Y (1995)); DNA Cloning, Volumes I and II (D. N.Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed. (1984));Mullis et al. U.S. Pat. No: 4,683,195; Nucleic Acid Hybridization (B. D.Hames & S. J. Higgins eds. (1984)), the treatise, Methods In Enzymology(Academic Press, Inc., N.Y.); Immunochemical Methods In Cell AndMolecular Biology (Mayer and Walker, eds., Academic Press, London(1987)); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weirand C. C. Blackwell, eds. (1986)); and Miller, J. Experiments inMolecular Genetics (Cold Spring Harbor Press, Cold Spring Harbor, N.Y.(1972)).

The invention is further illustrated by the following examples, whichshould not be construed as further limiting.

EXAMPLES Example 1 Ability of Oligonucleotide Compositions to InhibitCDK2 in A549 Cells

In this example, the ability of 5 different antisense oligonucleotidesindividually was compared with the ability of all 5 of the antisenseoligonucleotides transfected at one time for their ability to inhibitthe expression of CDK2 in A549 cells. The sequences of the 5 antisenseoligonucleotides used were: oligonucleotide 1 GCAGUAUACCUCUCGCUCUUGUCAA(SEQ ID NO: 8); oligonucleotide 2 UUUGGAAGUUCUCCAUGAAGCGCCA (SEQ ID NO:9); oligonucleotide 3 GUCCAAAGUCUGCUAGCUUGAUGGC (SEQ ID NO: 10);oligonucleotide 4 CCCAGGAGGAUUUCAGGAGCUCGGU (SEQ ID NO: 11);oligonucleotide 5 UAGAAGUAACUCCUGGCCACACCAC (SEQ ID NO: 12); reversecontrol AACUGUUCUCGCUCUCCAUAUGACG (SEQ ID NO: 13).

For transfection with antisense oligonucleotides A549 cells weremaintained in DMEM with high glucose (Gibco-BRL) supplemented with 10%Fetal Bovine Serum, 2 mM L-Glutamine, and 1× penicillin/streptomycin.

On the day before transfection 24-well plates were seeded with 30,000A549 cells per well. The cells were approximately 60% confluent at thestart of transfection, and were evenly distributed across the plate. Onthe day of transfection, a 10× stock of Lipofectamine 2000 (Invitrogen)was prepared in Opti-MEM (serum free media, Gibco-BRL). The dilutedlipid was allowed to stand at room temperature for 15 minutes. Theoptimal conditions for transfection of A549 cells were determined to be25 nM oligonucleotide complexed with 1 ug/mL Lipofectamine 2000. A 10×stock of each oligonucleotide to be used in the transfection was alsoprepared in Opti-MEM (10× concentration of oligonucleotide is 0.25 uM).Equal volumes of the 10× Lipofectamine 2000 stock and the 10×oligonucleotide solutions were mixed well and incubated for 15 minutesat room temperature to allow complexation of the oligonucleotide andlipid. The resulting mixture was 5×. After the 15 minutes ofcomplexation, four volumes of full growth media was added to theoligonucleotide/lipid complexes to make a 1× solution. The media wasaspirated from the cells, and 0.5 mL of the 1× oligonucleotide/lipidcomplexes was added to each well. The cells were not permitted to dryout during the changing of media. The cells were incubated for 16-24hours at 37° C. in a humidified CO₂ incubator. Cell pellets wereharvested for protein determination or RNA isolation. The Tables belowshow the results of the experiment.

Ratio of CDK2 expression Oligonucleotide to GAPDH expression StandardDeviation No transfection 1.481 0.242 FITC 1.004 0.203 1 0.233 0.041 20.231 0.058 3 0.198 0.015 4 0.193 0.065 5 0.673 0.232 Reverse Control0.749 0.079 Oligonucleotide 0.137 0.012 Composition

Percent Inhibition Compared Oligonucleotide to Reverse Control Notransfection 0 (−98%) FITC 0 (−34%) 1 69% 2 69% 3 74% 4 74% 5 10%Reverse Control  0% Oligonucleotide Composition 82%

The levels of expression of CDK2 were normalized to levels of GAPDH. Notransfection or transfection with a fluorescent control oligonucleotide(which targets luciferase) showed levels of 1 or higher. A reversesequence control oligonucleotide gave a level of about 0.8. Each of theindividual oligonucleotides (1-5) showed inhibition in CDK2 expression(with levels ranging from about 0.2 (about 70% inhibition compared tothe reverse control) to 0.65 (10% inhibition compared to the reversecontrol) for oligonucleotide number 5). All five of the oligonucleotidestransfected at once gave a level of less than about 0.2, about 82%inhibition compared to the reverse control. Thus, using only onetransfection, an oligonucleotide composition comprising five differentantisense oligonucleotides can be used to efficiently inhibit proteinsynthesis.

Example 2 Summary of Results of Experiments in which OligonucleotideCompositions were Tested on Thirty Different Genes

FIG. 1 shows a summary of the results of about 30 antisense inhibitionexperiments against about thirty different genes in cell culture.Antisense was transfected as described in Example 1 and inhibitionanalyzed by TaqMan® real time PCR using standard methods. In each casethe antisense inhibition was determined by comparison to a controloligonucleotide of the same chemistry that was not antisense to thetarget gene. Antisense compositions comprised 5-8 antisenseoligonucleotides that had been designed against each gene, andindividual oligonucleotides where compared to the mixtures of 5 or moreantisense oligonucleotides. For three target genes the mixtures did notwork well, and these data were eliminated from the analysis of themixtures. Remarkably, the mixtures inhibited approximately as well(81-vs 84%) as the best individual oligonucleotide. The averageinhibition of all individual oligonucleotides was much lower (56%), witha much higher variation. Thus, using the mixtures allows one to obtainhigh inhibition in the vast majority of cases (˜90% of the target genes)without first screening through individual oligonucleotides to selectthose which work best. Also, as evidenced by the increased variation inthe results obtained when individual oligonucleotides were used, in manycases the mixture was better than the best individual oligonucleotide.

Example 3 Ultramer Data for a Mixture of siRNA Complexes Targeting p53

HeLa cells were transfected with 50 nM siRNA complexed with 1 ug/mL ofLipofectamine 2000 for 24 hours. After 24 hours, cells were lysed andRNA isolated for analysis by RT-PCR. Seven siRNA complexes weretransfected that target a unique site of the p53 gene and a mixture ofall seven siRNAs (equal concentrations of each) called the “siRNAultramer.” The best siRNA complex inhibited the target by 87% and theultramer inhibited 69% compared to average of the controls. P53sequences (Antisense, Sense):

siRNA1: (SEQ ID NO: 14) CUGACUGCGGCUCCUCCAUTT (SEQ ID NO: 15)AUGGAGGAGCCGCAGUCAGTT siRNA2: (SEQ ID NO: 16) CUCACAACCUCCGUCAUGUTT(SEQ ID NO: 17) ACAUGACGGAGGUUGUGAGTT siRNA3: (SEQ ID NO: 18)GACCAUCGCUAUCUGAGCATT (SEQ ID NO: 19) UGCUCAGAUAGCGAUGGUCTT siRNA4:(SEQ ID NO: 20) GUACAGUCAGAGCCAACCUTT (SEQ ID NO: 21)AGGUUGGCUCUGACUGUACTT siRNA5: (SEQ ID NO: 22) ACCUCAAAGCUGUUCCGUCTT(SEQ ID NO: 23) GACGGAACAGCUUUGAGGUTT siRNA6: (SEQ ID NO: 24)CCUCAUUCAGCUCUCGGAATT (SEQ ID NO: 25) UUCCGAGAGCUGAAUGAGGTT siRNA7:(SEQ ID NO: 26) CCCUUCUGUCUUGAACAUGTT (SEQ ID NO: 27)CAUGUUCAAGACAGAAGGGTT.

Example 4 Ultramer Data for a Mixture of siRNA Complexes Targeting GTP20

Human Mesenchymal Stems cells (hMSC) were transfected with 2 ug/mLLipofectamine 2000 complexed to 400 nM siRNA (total concentration, forclarity in the mixture each individual oligomer was at 80 nM). FivesiRNA duplexes targeted to GTP20 (TD), one composition matched controlduplex (CD) and an equimolar mixture of each of the 5 oligos (“Mixture”)were transfected continuously for 24 hours and RNA was harvested usingthe RNA Catcher (Sequitur, Inc. Natick, Mass.). Expression of GTP20 mRNAwas quantified by TaqMan® and normalized to GAPDH Inhibition of 70% orgreater relative to the control duplex was achieved using TD5 (70%) andthe Ultramer (76%).

Human mesenchymal stem cells were plated at 15,000 per well in 48 welldishes and transfected 24 hours later. Lipofectamine 2000 was diluted inOpti-MEM to a 10× concentration of 20 ug/mL and incubated for 15minutes. Following incubation, lipid was complexed to siRNA duplexes byaddition of 10× lipid to an equal volume of 10× (4 uM) siRNA, andincubated for 15 minutes. 5× lipid/siRNA complexes were diluted to 1× bythe addition of MSC Differentiation Media. 250 ul of each 1× siRNAtreatment was added per well of 48 well dish. Each treatment was appliedto triplicate wells. Osteoblastic differentiation of MSC was inducedapproximately 4 hours after transfection. Cells were differentiated for4 days prior to RNA isolation.

Example 5 Ultramer Data for a Mixture of siRNA Complexes TargetingCbfa-1

Human Mesenchymal Stems cells (hMSC) were transfected with 2 ug/mLLipofectamine 2000 complexed to 400 nM siRNA (total concentration, inmixture each individual duplex was at 80 nM). Five targeted duplexes(TD), five control duplexes (CD), one equimolar mixture of all 5duplexes (“Mixture”) and one control Mixture(UC) were transfectedcontinuously for 72 hours. RNA was harvested 96 hours after transfectionusing the RNA Catcher. Expression of Cbfa-1 mRNA was quantified byTaqMan® and normalized to GAPDH Inhibition of 70% or greater relative tothe average of the control duplexes was achieved using TD4 (74%). TheMixture inhibited 70% relative to the Mixture Control.

Human mesenchymal stem cells were plated at 15,000 per well in 48 welldishes and transfected 24 hours later. Lipofectamine 2000 was diluted inOpti-MEM to a 10×. concentration of 20 ug/mL and incubated for 15minutes. Following incubation, lipid was complexed to siRNA duplexes byaddition of 10× lipid to an equal volume of 10× (4 uM) siRNA, andincubated for 15 minutes. 5× lipid/siRNA complexes were diluted to 1× bythe addition of MSC Differentiation Media. 250 ul of each 1× siRNAtreatment was added per well of 48 well dish. Each treatment was appliedto triplicate wells. Osteoblastic differentiation of MSC was inducedapproximately 4 hours after transfection. Cells were differentiated for4 days prior to RNA isolation. The following antisense sequences ofCbfa-1 siRNA duplexes were used (corresponding sense sequences where thecomplementary sequence with a 2 nt TT 3′ overhang, T's are DNA, allother nucleotides are RNA):

(SEQ ID NO: 28) TD1 (s18883): AUUUAAUAGCGUGCUGCCATT (SEQ ID NO: 29)TD2 (s18885): CUGUAAUCUGACUCUGUCCTT (SEQ ID NO: 30)TD3 (s18887): AAUAUGGUCGCCAAACAGATT (SEQ ID NO: 31)TD4 (s18889): GUCAACACCAUCAUUCUGGTT (SEQ ID NO: 32)TD5 (s18891): AGGUUUAGAGUCAUCAAGCTT (SEQ ID NO: 33)CD1 (s18884): ACCGUCGUGCGAUAAUUUATT (SEQ ID NO: 34)CD2 (s18886): CCUGUCUCAGUCUAAUGUCTT (SEQ ID NO: 35)CD3 (s18888): AGACAAACCGCUGGUAUAATT (SEQ ID NO: 36)CD4 (s18890): GGUCUUACUACCACAACUGTT (SEQ ID NO: 37)CD5 (s18892): CGAACUACUGAGAUUUGGATT.

Example 6 Data for a Mixture of Antisense Oligonucleotides Targeting PTPmu

Efficacy of all phosphorothioate DNA 25 nt antisense oligonucleotidestargeted against PTP mu mRNA in human lung carcinoma (A549) cells.Potent inhibition of mRNA was obtained following a 16 hour transfectionof A549 cells with 25 nM oligo. AS: antisense oligonucleotide; RC:reverse control; MIX: mixture of individual AS oligomers (total oligomerconcentration of 25 nM). Target mRNA quantity was normalized to GAPDH.

A549 cells at passage 3 were plated at 25,000 cells/well in 48 wellplates and incubated overnight in a humidified 5% CO₂ chamber (37° C.).A 250 nM solution of AS oligomer in Optimem-1 (Gibco BRL) was mixed withan equal volume of 10 ug/mL lipofectamine 2000 (InVitrogen) in Optimem-I(lipid solution was pre-incubated at 25 C. for 15 minutes).Oligomer-lipid complexes were formed by incubation at room temperaturefor 15 minutes. 4 volumes of DMEM plus 10% fetal serum medium was addedto the complexes and 250 ul of the diluted suspension was added tocells. The final concentration of oligomer was 25 nM. Following a 16 htransfection, cells were washed with PBS and poly A+ mRNA was isolatedusing Sequitur's mRNA Catcher. mRNA was quantified by real time RT-PCR(TaqMan®); automated data collection was with an ABI prism®. sequencedetection system. Data are normalized to GAPDH mRNA. Oligonucleotidesequences:

(SEQ ID NO: 38) AS1, CAUUCACCAGCAUGAGAGAACCUGA; (SEQ ID NO: 39)AS2, TCCCAGAGGCATTCACCAGCATGAG; (SEQ ID NO: 40)AS3, UCCAGAUAGGAUUCCCCAGUGGCCC; (SEQ ID NO: 41)AS4, CUGGUCAGGAGCACACUAAUCUCAU; (SEQ ID NO: 42)AS5, AGUCAAGGUGUUCACUUGCUCCCAA; (SEQ ID NO: 43)AS6, AAGUACUAAUGGCCAGUUCUGCCC; (SEQ ID NO: 44)AS7, CCCUGUAACCAGAGCCUGUCUCCUG; (SEQ ID NO: 45)AS8, GAGCUGGUCACCUUGAUUUCCUUCA; (SEQ ID NO: 46)AS9, CCAGGCAAGUCCCAAGUGUCCUCAU; (SEQ ID NO: 47)AS10, GAUGUCCUAACACCUUCACCUCAUC;MIX, equimolar solution of AS1 through AS10.

Example 7 Data for a Mixture of Antisense Oligonucleotides TargetingPTP-PEST

Efficacy of 25 nt phosphorothioate DNA antisense oligonucleotidestargeted against PTP-PEST mRNA in Human Umbilical Vein Endothelial Cells(HuVEC). Inhibition of mRNA was obtained following a 4 hour serum-freetransfection of cells with 200 nM oligo followed by a 14 h incubation inserum-containing medium. AS: antisense oligonucleotide; RC: reversecontrol; Mixture: mixture of individual AS oligomers (total oligoconcentration of 200 nM). Target mRNA quantity is normalized to GAPDH.

HuVEC cells at passage 3 were plated at 25,000 cells/well in 48 wellplates and incubated overnight in a humidified 5% CO₂ chamber (37° C.).A 2000 nM solution of AS oligomer in Optimem-I (Gibco BRL) was mixedwith an equal volume of 100 ug/mL Lipofectin (Gibco BRL) in Optimem-I(lipid solution was pre-incubated at 25° C. for 30 minutes).Oligomer-lipid complexes were formed by incubation at room temperaturefor 30 minutes. 4 volumes of Optimem-I (serum-free) was added to thecomplexes and 250 ul of the diluted suspension was added to cells. Fourhours later, the transfection complexes were aspirated and replaced with250 ul of EGM-2 complete serum medium (Clonetics/Biowhittaker).Following a 16 h transfection, cells were washed with PBS and poly A+mRNA was isolated using an mRNA Catcher (Sequitur, Inc.). mRNA wasquantified by real time RT-PCR (TaqMan®); automated data collection waswith an ABI prism® sequence detection system. Data are normalized toGAPDH mRNA.

(SEQ ID NO: 48) AS1, CCCAUUGUGGUCAGGACUCUUCAUGU; (SEQ ID NO: 49)AS2, UUCCCAUCUCAAAUUCU-CGGCAGGCU; (SEQ ID NO: 50)AS3, UGGCACAAAUGGCACCUGUUCUUCCU; (SEQ ID NO: 51)RC, GACUCCUUUAAGUAGGUCUCCCAGG-U.MIX, equimolar solution of AS1, AS2, and AS3.

Example 8 Data for a Mixture of Antisense Oligonucleotides TargetingPTP-eta

Efficacy of all phosphorothioate DNA 25 nt antisense oligonucleotidestargeted against PTP-eta mRNA in Normal Rat Kidney (NRK) cells.Inhibition of mRNA was obtained following an overnight transfection ofcells with 25 nM oligo. AS: antisense oligonucleotide; RC: reversecontrol; Mix: mixture of individual AS oligomers (total oligomerconcentration of 25 nM). Target mRNA quantity is normalized to GAPDH.

NRK cells at passage 5 were plated at 25,000 cells/well in 48 wellplates and incubated overnight in a humidified 5% CO2 chamber (37° C.).A 250 nM solution of AS oligomer in Optimem-I (Gibco BRL) was mixed withan equal volume of 10 ug/mL Lipofectamine 2000 (InVitrogen) in Optimem-I(lipid solution was pre-incubated at 25° C. for 30 minutes).Oligomer-lipid complexes were formed by incubation at room temperaturefor 15 minutes. 4 volumes of complete DMEM plus 5% bovine calf serumwere added to the complexes and 250 ul of the diluted suspension waslayered onto cells. The final oligomer concentration was 25 nM.Following a 16 h incubation, cells were washed with PBS and poly A+ mRNAwas isolated using Sequitur's mRNA Catcher. mRNA was quantified by realtime RT-PCR (TaqMan®); automated data collection was with an ABI Prism®sequence detection system. Data are normalized to GAPDH mRNA.

(SEQ ID NO: 52) AS1, ACCUGUGCACACAACCUGGCCCUGGU; (SEQ ID NO: 53)AS2, ACAGUAUACCGCAGCGUGUUUCCCUU; (SEQ ID NO: 54)AS3, GUCUCAUUGACUGUUCCCAAGGUGAU; (SEQ ID NO: 55)AS4, GCUCUACAAUCUGCAUCCGGUAAG-AU; (SEQ ID NO: 56)AS5, UCUGUGCCAUCUGCUGCUUGAGAAUU; (SEQ ID NO: 57)AS6, UGUUCACAGCUCGGAUGUCAGAAACU; (SEQ ID NO: 58)RC, UAAGAGUUCGUCGUCUACCGUGUCUU;MIX, equimolar solution of AS1 through AS6.

Equivalents

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

1-29. (canceled)
 30. An oligonucleotide composition comprising at leastthree different double-stranded RNA oligonucleotides targeted to atleast three different nucleotide sequences within a target gene.
 31. Amethod of inhibiting protein synthesis in a cell comprising contactingthe cell with at least three different double-stranded RNAoligonucleotides targeted to at least three different nucleotidesequences within a target gene.
 32. A method of identifying function ofa gene encoding a protein comprising: contacting the cell with at leastthree different double-stranded RNA oligonucleotides targeted to atleast three different nucleotide sequences within a target gene andassaying for a change in a detectable phenotype in the cell resultingfrom the inhibition of protein expression, to thereby determine thefunction of a gene.
 33. A method of making an oligonucleotidecomposition comprising: combining at least three differentdouble-stranded RNA oligonucleotides targeted to at least threedifferent nucleotide sequences within a target gene wherein, theindividual oligonucleotides are not separately tested for their abilityto inhibit protein synthesis prior to their incorporation into thecomposition.